From 9507710f601515268321642c4bd28ea89b7f3280 Mon Sep 17 00:00:00 2001 From: Joshua Klein Date: Fri, 30 Aug 2024 11:07:10 -0400 Subject: [PATCH] Remove python implementation from repository (#81) --- .github/workflows/python-tests.yml | 35 - implementations/python/.gitignore | 7 - implementations/python/README.md | 16 - .../python/bench/nist_msp_ftp_test.py | 61 - ...umanPlasma_2012-08_all.selected_head.sptxt | 604 - .../chinese_hamster_hcd_selected_head.msp | 1000 - ...chinese_hamster_hcd_selected_head.mzlb.txt | 1279 - implementations/python/examples/draw_entry.py | 27 - .../python/examples/first_n_entries.py | 42 - ...cac03860ff7453a821332ab4cff20f4_head.sptxt | 6322 ----- implementations/python/makefile | 13 - implementations/python/mzlib/__init__.py | 11 - implementations/python/mzlib/analyte.py | 233 - implementations/python/mzlib/annotation.py | 1 - implementations/python/mzlib/attributes.py | 827 - .../python/mzlib/backends/__init__.py | 8 - implementations/python/mzlib/backends/base.py | 702 - .../python/mzlib/backends/bibliospec.py | 208 - .../python/mzlib/backends/diann.py | 239 - .../python/mzlib/backends/encyclopedia.py | 183 - implementations/python/mzlib/backends/json.py | 511 - implementations/python/mzlib/backends/msp.py | 1692 -- .../python/mzlib/backends/spectronaut.py | 299 - .../python/mzlib/backends/sptxt.py | 87 - implementations/python/mzlib/backends/text.py | 916 - .../python/mzlib/backends/utils.py | 208 - implementations/python/mzlib/cluster.py | 57 - implementations/python/mzlib/defaults.py | 5 - implementations/python/mzlib/draw.py | 178 - .../python/mzlib/index/__init__.py | 3 - implementations/python/mzlib/index/base.py | 134 - implementations/python/mzlib/index/memory.py | 302 - implementations/python/mzlib/index/sql.py | 257 - implementations/python/mzlib/obo/psi-ms.obo | 22132 ---------------- implementations/python/mzlib/ontology.py | 69 - implementations/python/mzlib/ontology_term.py | 465 - implementations/python/mzlib/peak_list.py | 100 - implementations/python/mzlib/spectrum.py | 229 - .../python/mzlib/spectrum_library.py | 391 - .../mzlib/spectrum_library_collection.py | 381 - .../python/mzlib/spectrum_library_index.py | 357 - .../python/mzlib/tools/__init__.py | 0 implementations/python/mzlib/tools/cli.py | 211 - implementations/python/mzlib/tools/utils.py | 65 - .../mzlib/universal_spectrum_identifier.py | 281 - implementations/python/mzlib/utils.py | 19 - .../python/mzlib/validate/__init__.py | 0 .../python/mzlib/validate/level.py | 35 - .../python/mzlib/validate/object_rule.py | 88 - .../python/mzlib/validate/rules/__init__.py | 0 .../python/mzlib/validate/rules/all.json | 1578 -- .../python/mzlib/validate/rules/base.json | 173 - .../mzlib/validate/rules/consensus.json | 36 - .../python/mzlib/validate/rules/gold.json | 58 - .../python/mzlib/validate/rules/peptide.json | 32 - .../python/mzlib/validate/rules/silver.json | 48 - .../python/mzlib/validate/rules/single.json | 54 - .../python/mzlib/validate/rules/tmp/README.md | 10 - .../rules/tmp/excel_terms_to_json_rules.py | 71 - .../mzlib/validate/rules/tmp/terms.xlsx | Bin 25472 -> 0 bytes .../rules/validator-rules-schema.json | 216 - .../python/mzlib/validate/semantic_rule.py | 500 - .../python/mzlib/validate/validator.py | 385 - implementations/python/pyproject.toml | 49 - implementations/python/setup.cfg | 2 - implementations/python/tests/__init__.py | 0 implementations/python/tests/common.py | 14 - implementations/python/tests/test_cluster.py | 21 - .../python/tests/test_data/annotations.txt | 419 - .../test_data/bad_peak_annotations.mzlb.txt | 270 - .../chinese_hamster_hcd_selected_head.msp | 1000 - ...hinese_hamster_hcd_selected_head.mzlb.json | 4647 ---- ...chinese_hamster_hcd_selected_head.mzlb.txt | 1279 - .../tests/test_data/clusters_example.mzlb | 142 - .../complex_interpretations.mzlb.txt | 15 - ...lex_interpretations_with_members.mzlb.json | 141 - ...plex_interpretations_with_members.mzlb.txt | 21 - .../tests/test_data/generate_annotations.py | 21 - .../human_serum.head.spectronaut.tsv | 145 - ...04_canonical_sall_pv_plasma.head.diann.tsv | 147 - implementations/python/tests/test_index.py | 47 - implementations/python/tests/test_library.py | 17 - .../python/tests/test_library_backend.py | 98 - .../python/tests/test_msp_attributes.py | 16 - implementations/python/tests/test_spectrum.py | 32 - implementations/python/tests/test_validate.py | 39 - 86 files changed, 53033 deletions(-) delete mode 100644 .github/workflows/python-tests.yml delete mode 100644 implementations/python/.gitignore delete mode 100644 implementations/python/README.md delete mode 100644 implementations/python/bench/nist_msp_ftp_test.py delete mode 100644 implementations/python/examples/HumanPlasma_2012-08_all.selected_head.sptxt delete mode 100644 implementations/python/examples/chinese_hamster_hcd_selected_head.msp delete mode 100644 implementations/python/examples/chinese_hamster_hcd_selected_head.mzlb.txt delete mode 100644 implementations/python/examples/draw_entry.py delete mode 100644 implementations/python/examples/first_n_entries.py delete mode 100644 implementations/python/examples/massivekb_human_speclib_3cac03860ff7453a821332ab4cff20f4_head.sptxt delete mode 100644 implementations/python/makefile delete mode 100644 implementations/python/mzlib/__init__.py delete mode 100644 implementations/python/mzlib/analyte.py delete mode 100644 implementations/python/mzlib/annotation.py delete mode 100644 implementations/python/mzlib/attributes.py delete mode 100644 implementations/python/mzlib/backends/__init__.py delete mode 100644 implementations/python/mzlib/backends/base.py delete mode 100644 implementations/python/mzlib/backends/bibliospec.py delete mode 100644 implementations/python/mzlib/backends/diann.py delete mode 100644 implementations/python/mzlib/backends/encyclopedia.py delete mode 100644 implementations/python/mzlib/backends/json.py delete mode 100644 implementations/python/mzlib/backends/msp.py delete mode 100644 implementations/python/mzlib/backends/spectronaut.py delete mode 100644 implementations/python/mzlib/backends/sptxt.py delete mode 100644 implementations/python/mzlib/backends/text.py delete mode 100644 implementations/python/mzlib/backends/utils.py delete mode 100644 implementations/python/mzlib/cluster.py delete mode 100644 implementations/python/mzlib/defaults.py delete mode 100644 implementations/python/mzlib/draw.py delete mode 100644 implementations/python/mzlib/index/__init__.py delete mode 100644 implementations/python/mzlib/index/base.py delete mode 100644 implementations/python/mzlib/index/memory.py delete mode 100644 implementations/python/mzlib/index/sql.py delete mode 100644 implementations/python/mzlib/obo/psi-ms.obo delete mode 100644 implementations/python/mzlib/ontology.py delete mode 100644 implementations/python/mzlib/ontology_term.py delete mode 100644 implementations/python/mzlib/peak_list.py delete mode 100644 implementations/python/mzlib/spectrum.py delete mode 100644 implementations/python/mzlib/spectrum_library.py delete mode 100644 implementations/python/mzlib/spectrum_library_collection.py delete mode 100644 implementations/python/mzlib/spectrum_library_index.py delete mode 100644 implementations/python/mzlib/tools/__init__.py delete mode 100644 implementations/python/mzlib/tools/cli.py delete mode 100644 implementations/python/mzlib/tools/utils.py delete mode 100644 implementations/python/mzlib/universal_spectrum_identifier.py delete mode 100644 implementations/python/mzlib/utils.py delete mode 100644 implementations/python/mzlib/validate/__init__.py delete mode 100644 implementations/python/mzlib/validate/level.py delete mode 100644 implementations/python/mzlib/validate/object_rule.py delete mode 100644 implementations/python/mzlib/validate/rules/__init__.py delete mode 100644 implementations/python/mzlib/validate/rules/all.json delete mode 100644 implementations/python/mzlib/validate/rules/base.json delete mode 100644 implementations/python/mzlib/validate/rules/consensus.json delete mode 100644 implementations/python/mzlib/validate/rules/gold.json delete mode 100644 implementations/python/mzlib/validate/rules/peptide.json delete mode 100644 implementations/python/mzlib/validate/rules/silver.json delete mode 100644 implementations/python/mzlib/validate/rules/single.json delete mode 100644 implementations/python/mzlib/validate/rules/tmp/README.md delete mode 100644 implementations/python/mzlib/validate/rules/tmp/excel_terms_to_json_rules.py delete mode 100644 implementations/python/mzlib/validate/rules/tmp/terms.xlsx delete mode 100644 implementations/python/mzlib/validate/rules/validator-rules-schema.json delete mode 100644 implementations/python/mzlib/validate/semantic_rule.py delete mode 100644 implementations/python/mzlib/validate/validator.py delete mode 100644 implementations/python/pyproject.toml delete mode 100644 implementations/python/setup.cfg delete mode 100644 implementations/python/tests/__init__.py delete mode 100644 implementations/python/tests/common.py delete mode 100644 implementations/python/tests/test_cluster.py delete mode 100644 implementations/python/tests/test_data/annotations.txt delete mode 100644 implementations/python/tests/test_data/bad_peak_annotations.mzlb.txt delete mode 100644 implementations/python/tests/test_data/chinese_hamster_hcd_selected_head.msp delete mode 100644 implementations/python/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.json delete mode 100644 implementations/python/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.txt delete mode 100644 implementations/python/tests/test_data/clusters_example.mzlb delete mode 100644 implementations/python/tests/test_data/complex_interpretations.mzlb.txt delete mode 100644 implementations/python/tests/test_data/complex_interpretations_with_members.mzlb.json delete mode 100644 implementations/python/tests/test_data/complex_interpretations_with_members.mzlb.txt delete mode 100644 implementations/python/tests/test_data/generate_annotations.py delete mode 100644 implementations/python/tests/test_data/human_serum.head.spectronaut.tsv delete mode 100644 implementations/python/tests/test_data/phl004_canonical_sall_pv_plasma.head.diann.tsv delete mode 100644 implementations/python/tests/test_index.py delete mode 100644 implementations/python/tests/test_library.py delete mode 100644 implementations/python/tests/test_library_backend.py delete mode 100644 implementations/python/tests/test_msp_attributes.py delete mode 100644 implementations/python/tests/test_spectrum.py delete mode 100644 implementations/python/tests/test_validate.py diff --git a/.github/workflows/python-tests.yml b/.github/workflows/python-tests.yml deleted file mode 100644 index 3e23788..0000000 --- a/.github/workflows/python-tests.yml +++ /dev/null @@ -1,35 +0,0 @@ -name: Python tests - -on: push - -jobs: - test: - runs-on: ${{ matrix.os }} - strategy: - matrix: - os: [ubuntu-latest, windows-latest, macos-latest] - python-version: ["3.8", "3.9", "3.10"] - steps: - - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v3 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install flake8 pytest - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 implementations/python --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 implementations/python --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: Install python package - run: | - pip install --editable implementations/python[test] - - name: Test with pytest - env: - MZSPECLIB_PEAK_ANNOTATION_SCHEMA_LOCATION: "specification/peak-annotation-format/annotation-schema.json" - run: | - pytest -r a diff --git a/implementations/python/.gitignore b/implementations/python/.gitignore deleted file mode 100644 index 4786091..0000000 --- a/implementations/python/.gitignore +++ /dev/null @@ -1,7 +0,0 @@ -*.pyc -__pycache__ -*egg-info* -*.ipynb -examples/*splindex -.coverage -htmlcov/ \ No newline at end of file diff --git a/implementations/python/README.md b/implementations/python/README.md deleted file mode 100644 index b519191..0000000 --- a/implementations/python/README.md +++ /dev/null @@ -1,16 +0,0 @@ -# PSI Spectral Library format - Python implementation - -For development, run: -```sh -pip install --editable . -``` - -Or from the root of this repository: -```sh -pip install --editable implementations/python -``` - -Test with -``` -pytest -```` diff --git a/implementations/python/bench/nist_msp_ftp_test.py b/implementations/python/bench/nist_msp_ftp_test.py deleted file mode 100644 index 521332a..0000000 --- a/implementations/python/bench/nist_msp_ftp_test.py +++ /dev/null @@ -1,61 +0,0 @@ -#!/usr/bin/env python -import io -import tarfile -import pprint - -from urllib.request import urlopen - -from mzlib.backends import msp -from mzlib import annotation - - -urls = [ - "https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_tryp_good.msp.tar.gz", - "https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2019_02_14/human_hcd_labelfree_phospho_selected_passed.msp.tar.gz", - "https://chemdata.nist.gov/download/peptide_library/libraries/cptaclib/2015/cptac2_human_hcd_itraq_phospho_selected.msp.tar.gz", - "https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2022_03_16/cptac3_tmt_selected_passed_best.msp.tar.gz", - "https://chemdata.nist.gov/download/peptide_library/libraries/sigmaups1/ION_TRAP/2011_05_24/2011_05_24_sigmaups1_consensus_final_true_lib.tar.gz", - "https://chemdata.nist.gov/download/peptide_library/libraries/proteins/ion_trap/bsa/strict/2011_04_01/2011_04_01_bsa_consensus_final_true_lib.tar.gz", - "https://chemdata.nist.gov/download/peptide_library/libraries/cptaclib/2015/cptac2_mouse_hcd_itraq_phospho_selected.msp.tar.gz", -] - - -def open_url(url: str, buffer_size: int=2 ** 20): - buffer = io.BytesIO( - urlopen(url).read(buffer_size) - ) - - arc = tarfile.open( - fileobj=buffer, - mode='r:gz') - - ti = arc.firstmember - fh = arc.extractfile(ti) - return fh - - -def check_url(url: str, n_spectra_to_read: int=100, track_unknown_attribute_values: bool=True): - buffer = open_url(url) - backend = msp.MSPSpectralLibrary(buffer, read_metadata=False, create_index=False) - - if track_unknown_attribute_values: - backend.unknown_attributes = msp.UnknownKeyValueTracker() - for i, spec in enumerate(backend.read()): - for (mz, inten, annots, aggs) in spec.peak_list: - for annot in annots: - if isinstance(annot, annotation.InvalidAnnotation): - print(f"Failed to parse {annot} with m/z {mz}") - if i >= n_spectra_to_read: - break - - pprint.pprint(backend.summarize_parsing_errors()) - - -def main(): - for url in urls: - print(f"Testing URL {url}") - check_url(url) - - -if __name__ == "__main__": - main() diff --git a/implementations/python/examples/HumanPlasma_2012-08_all.selected_head.sptxt b/implementations/python/examples/HumanPlasma_2012-08_all.selected_head.sptxt deleted file mode 100644 index f0c2797..0000000 --- a/implementations/python/examples/HumanPlasma_2012-08_all.selected_head.sptxt +++ /dev/null @@ -1,604 +0,0 @@ -### HumanAllPublic_2012-07_all.sptxt (Text version of HumanAllPublic_2012-07_all.splib) -### SpectraST (version 4.0, TPP v4.6 OCCUPY rev 0, Build 201208271324 (linux)) -### -### COMPILE FROM "/regis/sbeams/archive/blin/PID_serum/PID_serum/XTK_ipi.HUMAN.v3.71.targetdecoy/RAW.splib" UNION ... "/regis/sbeams/archive/msnyder/iPOP/PBMC2011_SerumProteomics_r3/XTK/RAW.splib" [CONSENSUS;r=1;I=;_QUO=0.6;_XNR=100;_WGT=SN;_DIS=TRUE;_XPK=150;_XPU=300;_BDN=FALSE;_TBD=FALSE] -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/blin/PID_serum/PID_serum/XTK_ipi.HUMAN.v3.71.targetdecoy/raw_P0.9995850000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP01/hupo1_b1-cit_cam/SPC_HsNIST2.0/raw_P0.9984800000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP01/hupo1_b1-edta_cam/SPC_HsNIST2.0/raw_P0.9990010000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP01/hupo1_b1-hep_cam/SPC_HsNIST2.0/raw_P0.9990620000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP01/hupo1_b1-serum_cam/SPC_HsNIST2.0/raw_P0.9984360000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP01/hupo1_b2-cit_cam/SPC_HsNIST2.0/raw_P0.9990780000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP01/hupo1_b2-edta_cam/SPC_HsNIST2.0/raw_P0.9986420000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP01/hupo1_b2-hep_cam/SPC_HsNIST2.0/raw_P0.9987950000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP01/hupo1_b2-serum_cam/SPC_HsNIST2.0/raw_P0.9989710000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP01/hupo1_b3-serum_cam/SPC_HsNIST2.0/raw_P0.9987520000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP12/HUPO12_run31/SPC_HsNIST2.0/raw_P0.9991580000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP12/HUPO12_run32/SPC_HsNIST2.0/raw_P0.9988040000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP12/HUPO12_run33/SPC_HsNIST2.0/raw_P0.9988520000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP12/HUPO12_run34/SPC_HsNIST2.0/raw_P0.9987360000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP17/hupo17_b1-serum_cam/SPC_HsNIST2.0/raw_P0.9994490000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP22/HUPO22_M_CA_S/SPC_HsNIST2.0/raw_P0.9994160000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP28/HUPO28_b1-CIT/SPC_HsNIST2.0/raw_P0.9985520000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP28/HUPO28_b1-SERUM/SPC_HsNIST2.0/raw_P0.9987550000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP28/HUPO28_b2-CIT/SPC_HsNIST2.0/raw_P0.9988590000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP28/HUPO28_b2-SERUM/SPC_HsNIST2.0/raw_P0.9987430000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP28/HUPO28_b3-CIT/SPC_HsNIST2.0/raw_P0.9986470000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP28/HUPO28_b3-SERUM/SPC_HsNIST2.0/raw_P0.9985820000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP28/HUPO28_Ref-CIT/SPC_HsNIST2.0/raw_P0.9987100000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP28/HUPO28_Ref-SERUM/SPC_HsNIST2.0/raw_P0.9984740000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP29/HUPO29_b1-CIT_1/SPC_HsNIST2.0/raw_P0.9990700000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP29/HUPO29_b1-CIT_win1/SPC_HsNIST2.0/raw_P0.9993240000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP29/HUPO29_b1-CIT_win2/SPC_HsNIST2.0/raw_P0.9991590000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP29/HUPO29_b1-EDTA_1/SPC_HsNIST2.0/raw_P0.9992210000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP29/HUPO29_b1-EDTA_win1/SPC_HsNIST2.0/raw_P0.9992910000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP29/HUPO29_b1-EDTA_win2/SPC_HsNIST2.0/raw_P0.9989870000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP29/HUPO29_b1-HEP/SPC_HsNIST2.0/raw_P0.9988520000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP29/HUPO29_b1-SERUM/SPC_HsNIST2.0/raw_P0.9982730000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP33/HUPOPPP33_Deca/SPC_HsNIST2.0/raw_P0.9991960000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP34/HUPO34/SPC_HsNIST2.0/raw_P0.9991510000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP34/HUPO34_b1-SERUM/SPC_HsNIST2.0/raw_P0.9994470000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP37/HUPO37_b1-HEP_2LCQ/SPC_HsNIST2.0/raw_P0.9990410000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP40/HUPO40/SPC_HsNIST2.0/raw_P0.9983940000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP46/hupo46_c1-serum_cam/SPC_HsNIST2.0/raw_P0.9980500000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP46/hupo46_reference_cam/SPC_HsNIST2.0/raw_P0.9989810000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP53/hupo53_reference_cam/SPC_HsNIST2.0/raw_P0.9993350000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/edeutsch/HUPOPPP55/hupo55_b1-cit_cam/SPC_HsNIST2.0/raw_P0.9992060000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams4/archive/wqian/HsPlasma/HsPlasma_tryp_nonalkylated/SPC_HsNIST2.0/raw_P0.9991090000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams4/archive/tconrads/NCIHumanSerum/NCIHumanSerum/SPC_HsNIST2.0/raw_P0.9993680000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/mpeitsch/NovartisPlasma/MicroProt/SPC_HsNIST2.0/raw_P0.9993180000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/pmallick/Plasma/BOBFreezeThaw/SPC_HsNIST2.0/raw_P0.9982270000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/pmallick/Plasma/BOB2L/SPC_HsNIST2.0/raw_P0.9984330000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/pmallick/Plasma/BOB2L_ISB/SPC_HsNIST2.0/raw_P0.9981950000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/pmallick/Plasma/BOB2H_ISB/SPC_HsNIST2.0/raw_P0.9983590000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/pmallick/Plasma/BOB_Sensitivity/SPC_HsNIST2.0/raw_P0.9982870000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/ovitek/LatinSquare/LS_SpikedSerum/SPC_HsNIST2.0/raw_P.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/mpeitsch/NovartisPlasma/MicroProt2/SPC_HsNIST2.0/raw_P0.9987330000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/pwilmarth/WilmarthSamples/Wilmarth_human_serum1/SPC_HsNIST2.0/raw_P0.9986970000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/apaulovich/serum_fractionation/15_clinprot_c3/SPC_HsNIST2.0/raw_P0.9988830000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/apaulovich/serum_fractionation/16_clinprot_c8/SPC_HsNIST2.0/raw_P0.9988470000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/apaulovich/serum_fractionation/17_wcx/SPC_HsNIST2.0/raw_P0.9984950000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/apaulovich/serum_fractionation/18_size/SPC_HsNIST2.0/raw_P0.9989690000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/apaulovich/serum_fractionation/19_proteinag/SPC_HsNIST2.0/raw_P0.9992020000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/apaulovich/serum_fractionation/20_cys/SPC_HsNIST2.0/raw_P0.9982920000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/apaulovich/serum_fractionation/21_unfract/SPC_HsNIST2.0/raw_P0.9977250000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/apaulovich/serum_fractionation/22_mars/SPC_HsNIST2.0/raw_P0.9989770000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/apaulovich/serum_fractionation/01_glyco/XTK_ipi.HUMAN.v3.71.targetdecoy/raw_P0.9997200000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/dsmith/Plasma/Normal_LCQ_Cys_May04/SPC_HsNIST2.0/raw_P0.9990910000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/dsmith/Plasma/Normal_LCQ_NoCys_May04/SPC_HsNIST2.0/raw_P0.9994750000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/dsmith/Plasma/Normal_LCQ_NoCys_Oct04/SPC_HsNIST2.0/raw_P0.9989330000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/dsmith/Plasma/Normal_LTQ_Cys_Dec04/SPC_HsNIST2.0/raw_P0.9986240000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/dsmith/Plasma/Trauma_LTQ_Cys_Apr05/SPC_HsNIST2.0/raw_P0.9987230000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/dsmith/Plasma/Trauma_LTQ_Cys_Mar05/SPC_HsNIST2.0/raw_P0.9988170000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/dsmith/Plasma/Trauma_LTQ_NoCys_Mar05/SPC_HsNIST2.0/raw_P0.9992620000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/dsmith/Plasma/Trauma_LTQ_NonGlyco_Apr05/SPC_HsNIST2.0/raw_P0.9993260000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/pmallick/Plasma/PPP-2/SPC_HsNIST2.0/raw_P0.9977800000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/hzhang/serum_glycoproteins/breakfast_qtof08/XTK_HsIPI3.54_Bswap/raw_P0.9995140000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/hzhang/serum_glycoproteins/caex_qtof08/XTK_HsIPI3.54_Bswap/raw_P0.9993570000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/hzhang/serum_glycoproteins/cat_ex_qtof/XTK_HsIPI3.54_Bswap/raw_P0.9994980000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/hzhang/serum_glycoproteins/cation_ex_lcq/XTK_HsIPI3.54_Bswap/raw_P0.9994650000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/hzhang/serum_peo_peptides/serum_peo_peptides/XTK_ipi.HUMAN.v3.71.targetdecoy/raw_P0.9997670000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/jmalmstr/serum_IEF/serum_FFE_2006_LTQ-FT/XTK_HsIPI3.54_Bswap/raw_P0.9987420000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/jmalmstr/serum_IEF/serum_FFE_2006_LTQ/XTK_HsIPI3.54_Bswap/raw_P0.9994860000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/jmalmstr/serum_IEF/serum_OGE_2006_LTQ-FT/XTK_HsIPI3.54_Bswap/raw_P0.9994760000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/jmalmstr/serum_IEF/serum_OGE_2006_LTQ/XTK_HsIPI3.54_Bswap/raw_P0.9993880000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/jmalmstr/lg_scale_serum/2007_08_09/XTK_HsIPI3.54_Bswap/raw_P0.9994520000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/jmalmstr/lg_scale_serum/SEC_OGE_II/XTK_HsIPI3.54_Bswap_LTQ/raw_P0.9992340000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/jmalmstr/lg_scale_serum/SEC_OGE_II/XTK_HsIPI3.54_Bswap_LTQ-FT/raw_P0.9992340000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/jmalmstr/lg_scale_serum/SEC_OGE_II/XTK_HsIPI3.54_Bswap_Agilent-IT/raw_P0.9993060000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/jmalmstr/lg_scale_serum/IEF_GeH/XTK_HsIPI3.54_Bswap/raw_P0.9992190000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/jwatts/HsGlycoPlasma35indiv/HsGlycoPlasma35indiv/XTK_HsIPI3.54_Bswap/raw_P0.9994720000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/rossola/HUPO-ISB/b1-CIT_glyco_lcq/XTK_HsIPI3.54_Bswap/raw_P0.9990440000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/rossola/HUPO-ISB/b1-CIT_glyco_qstar/XTK_HsIPI3.54_Bswap/raw_P0.9984630000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/rossola/HUPO-ISB/NIBSC_glyco_lcq/XTK_HsIPI3.54_Bswap/raw_P0.9993180000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/rossola/HUPO-ISB/NIBSC_glyco_qstar/XTK_HsIPI3.54_Bswap/raw_P0.9990490000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/dsmith/Plasma/Normal_LCQ_Glyco_Jun04/XTK_HsIPI3.54_Bswap/raw_P0.9991280000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/dsmith/Plasma/Normal_LTQ_Glyco_Nov04/XTK_HsIPI3.54_Bswap/raw_P0.9989700000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/dsmith/Plasma/Trauma_LTQ_Glyco_Apr05/XTK_HsIPI3.54_Bswap/raw_P0.9990290000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams/archive/dsmith/Plasma/Trauma_LTQ_Glyco_Mar05/XTK_HsIPI3.54_Bswap/raw_P0.9990750000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams4/archive/wqian/HsPlasma/HsPlasma_tryp_alkylated/SPC_HsNIST2.0/raw_P0.9990790000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_01/raw_P0.9979940000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_02/raw_P0.9980180000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_03/raw_P0.9979160000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_04/raw_P0.9979270000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_05/raw_P0.9980410000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_06/raw_P0.9982730000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_07/raw_P0.9982880000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_08/raw_P0.9986170000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_09/raw_P0.9981330000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_10/raw_P0.9977760000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_11/raw_P0.9979200000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_12/raw_P0.9981200000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_13/raw_P0.9987260000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_14/raw_P0.9975260000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_15/raw_P0.9987790000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_16/raw_P0.9983490000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_17/raw_P0.9981430000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_18/raw_P0.9984940000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_19/raw_P0.9979110000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_20/raw_P0.9982530000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_21/raw_P0.9982670000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_22/raw_P0.9979250000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_23/raw_P0.9981350000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_24/raw_P0.9981400000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_25/raw_P0.9977960000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_26/raw_P0.9977780000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_27/raw_P0.9980720000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_28/raw_P0.9981740000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_29/raw_P0.9986190000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_30/raw_P0.9980200000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_31/raw_P0.9981240000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_32/raw_P0.9983750000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_33/raw_P0.9982250000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_34/raw_P0.9983490000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_35/raw_P0.9980140000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_36/raw_P0.9981480000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_37/raw_P0.9980570000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_38/raw_P0.9979180000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_39/raw_P0.9979220000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/nobackup/Roche/Combined_40/raw_P0.9982690000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/shanash/hanash_HsPlasma/HsPlasma_IP0023/iprophet_1Dec10/raw_P0.9975060000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/shanash/hanash_HsPlasma/HsPlasma_IP0028/iprophet_1Dec10/raw_P0.9978820000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/shanash/hanash_HsPlasma/HsPlasma_IP0029/iprophet_1Dec10/raw_P0.9979920000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/shanash/hanash_HsPlasma/HsPlasma_IP0055/iprophet_1Dec10/raw_P0.9981560000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/shanash/hanash_HsPlasma/HsPlasma_IP0056/iprophet_1Dec10/raw_P0.9980260000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/shanash/hanash_HsPlasma/HsPlasma_IP0018/XTK-ISB/raw_P0.9992800000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/shanash/hanash_HsPlasma/HsPlasma_IP0021/XTK-AWS/raw_P0.9990190000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/shanash/hanash_HsPlasma/HsPlasma_IP0027/XTK-ISB/raw_P0.9993730000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/shanash/hanash_HsPlasma/HsPlasma_IP0049/XTK-AWS/raw_P0.9991240000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/shanash/hanash_HsPlasma/HsPlasma_IP0050/XTK-REG/raw_P0.9991300000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/shanash/hanash_HsPlasma/HsPlasma_IP0083/XTK-REG/raw_P0.9992400000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/shanash/hanash_HsPlasma/HsPlasma_IP0089/XTK-REG/raw_P0.9992750000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/shanash/hanash_HsPlasma/HsPlasma_IP0111/XTK-REG/raw_P0.9992570000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/shanash/hanash_HsPlasma/HsPlasma_IP0112/XTK-REG/raw_P0.9993110000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams2/archive/shanash/hanash_HsPlasma/HsPlasma_IP0113/XTK-REG/raw_P0.9993650000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/archive/msnyder/iPOP/PBMC2011_SerumProteomics_r1/XTK/raw_P0.9996730000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/archive/msnyder/iPOP/PBMC2011_SerumProteomics_r2/XTK/raw_P0.9996860000.msp" -### > RAW.splib : IMPORT FROM MSP "/regis/sbeams6/archive/msnyder/iPOP/PBMC2011_SerumProteomics_r3/XTK/raw_P0.9996930000.msp" -### === -Name: AAFIC[339]PGSSR/2 -LibID: 0 -MW: 1245.6576 -PrecursorMZ: 622.8288 -Status: Normal -FullName: X.AAFIC[339]PGSSR.X/2 (CID) -Comment: AvePrecursorMz=623.1846 BinaryFileOffset=18522 CollisionEnergy=0.0 FracUnassigned=0.00,0/5;0.11,5/20;0.21,75/150 Inst=1/UNKNOWN,1 MassDiff=0.3690 Mods=1/4,C,ICAT-C:13C(9) NAA=10 NISTProtein=3/IPI00022488/ENSP00000265983/P02790 NMC=0 NTT=1 Nreps=1/1 OrigMaxIntensity=5e+06 Parent=622.829 Pep=Semi-tryp PrecursorIntensity=9.2e+06 Prob=1.0000 Protein=1/3/IPI00022488/ENSP00000265983/P02790 RawSpectrum=serum41.01324.01324 RetentionTime=2960.9,2960.9,2960.9 Sample=1/PID_serum,1,1 Se=1^K1:pb=0.9997/0,fv=5.8759/0,hs=542/0,ns=359/0,ex=0.0540/0 Spec=Single TotalIonCurrent=3.4e+07 -NumPeaks: 150 -192.1223 90.2 ? -216.9937 272.9 y2-46/0.85 -233.1068 76.5 ? -234.3250 106.3 y5-36^2/0.20,y5-35^2/-0.29 -238.2444 136.4 ? -244.9837 643.1 y2-17/-0.14,y2-18/0.84 -245.9797 195.2 y2-17i/-0.14 -260.1537 88.3 ? -260.9393 138.9 ? -262.0157 228.0 y2/-0.14,a3/-0.14 -271.1136 140.0 ? -277.7427 124.8 ? -289.9490 877.9 b3/-0.20 -322.2329 113.9 ? -325.1179 178.6 ? -329.7177 146.2 ? -331.8362 118.4 y3-17/-0.32,y3-18/0.66 -349.1229 397.6 y3/-0.06 -358.9430 152.5 y6-127^2/0.73 -368.1693 101.8 b6-102^2/-0.86 -375.1040 500.6 a4/-0.14 -376.0346 486.9 a4i/-0.20 -387.2635 79.7 y4-18/-0.93 -391.2631 125.3 ? -394.1519 116.5 ? -396.2213 121.9 ? -402.2014 76.4 ? -403.0586 595.6 b4/-0.18,y6-36^2/-0.65 -404.0656 67.8 b4i/-0.17,y6-35^2/-0.13 -406.2118 169.0 y4/0.01,a6^2/-0.02 -412.9069 235.1 y6-18^2/0.20,y6-17^2/-0.30 -418.3030 101.7 ? -420.0251 355.9 b6^2/-0.21 -421.8215 712.6 y6^2/0.11 -422.8484 185.6 ? -424.6622 124.6 ? -429.1541 99.1 b8-127^2/0.40 -437.6237 230.9 ? -443.1688 65.1 ? -447.9781 118.5 b7^2/-0.76 -451.3279 80.5 ? -453.2460 88.9 ? -454.1644 96.0 ? -456.4361 63.8 y7-44^2/0.17,y5-46/-0.82 -465.1915 123.0 ? -466.0222 83.3 ? -469.6919 117.5 y7-17^2/-0.05,y7-18^2/0.44 -472.0148 75.4 b9-127^2/-0.26 -478.3409 2246.0 y7^2/0.08,a8^2/0.08 -479.1372 341.2 y7^2i/0.38 -484.2420 96.4 b8-17^2/0.50,b9-102^2/-0.33 -485.3043 253.6 y5-18/0.06 -486.2792 63.6 y5-17/0.05 -503.3000 10000.0 y5/0.04 -504.3158 1674.1 y5i/0.06 -510.1474 99.0 ? -517.1841 114.1 b9-36^2/-0.58 -524.8276 199.9 ? -529.2021 99.7 y8-46^2/0.41 -530.2327 87.8 y8-44^2/0.44 -536.2212 68.5 b9^2/0.45,y9-102^2/0.11 -538.0092 1158.6 ? -538.9526 271.0 ? -540.1929 158.2 ? -543.2502 642.3 y8-17^2/-0.03,y8-18^2/0.46 -544.0131 174.5 b9+18^2/-0.77 -551.7622 3331.6 y8^2/-0.03 -552.4160 1341.5 y8^2i/0.12 -553.5625 154.6 ? -555.8557 161.4 ? -556.6887 90.5 ? -557.6233 532.6 ? -565.4131 69.6 y9-44^2/0.10 -567.0731 587.0 ? -568.2148 70.9 ? -569.3860 96.6 y9-36^2/0.09,y9-35^2/-0.41 -571.4934 1158.4 p-102^2/-0.14 -573.3652 71.0 ? -578.1287 88.0 y9-18^2/-0.18 -578.9750 247.3 y9-17^2/0.18 -583.1458 270.7 ? -587.4165 244.4 y9^2/0.11 -591.7673 332.6 ? -592.8489 111.1 ? -594.1875 66.0 ? -595.4412 130.7 ? -600.4207 595.4 p-44^2/-0.41,p-46^2/0.59 -601.2819 197.8 ? -603.4592 70.3 ? -604.5455 354.0 p-36^2/-0.27 -605.6394 799.2 p-35^2/0.33 -611.3955 67.4 ? -612.2014 297.7 ? -613.1069 129.4 ? -614.1523 962.6 p-17^2/-0.16,p-18^2/0.33 -626.1543 78.8 ? -629.2721 64.6 ? -636.2925 80.5 ? -637.9956 136.8 ? -639.2954 644.3 b5-102/-0.70 -640.3325 206.8 b5-102i/-0.67 -641.6898 76.1 ? -654.4221 122.1 ? -667.9453 146.9 ? -680.2054 704.7 ? -690.1030 90.6 ? -696.6183 102.8 ? -697.3414 281.3 ? -698.3778 81.7 ? -699.0697 93.9 ? -701.5941 209.6 ? -706.5812 804.1 ? -707.5693 99.8 ? -709.8387 103.1 ? -724.3126 204.0 ? -725.1575 4140.5 b5-17/-0.22 -726.2451 1194.4 b5-17i/-0.13 -727.4183 69.1 b5-17i/0.04 -742.1533 1395.9 b5/-0.25 -743.2408 384.7 b5i/-0.16 -744.0972 63.6 b5i/-0.30 -765.0631 136.3 ? -772.3175 74.2 ? -807.5458 66.6 y6-35/0.16 -817.8947 164.5 ? -819.8468 141.0 ? -825.3601 416.7 y6-17/-0.04 -833.4131 247.6 ? -835.1906 194.2 ? -841.2793 285.7 ? -842.4032 5464.2 y6/-0.02 -843.4612 1148.3 y6i/0.04 -844.3485 169.5 y6i/-0.08 -853.5157 106.2 y7-102/0.41 -878.4762 162.3 ? -880.1658 358.2 b7-17/0.72,b8-102/-0.94 -896.3263 137.2 b7/-0.15 -911.0426 147.0 y7-44/-0.48 -917.0878 64.2 ? -925.8971 73.4 ? -955.4207 767.2 y7/-0.09,a8/-0.09 -956.3523 136.6 y7i/-0.16 -965.7443 159.7 b8-18/0.25,b8-17/-0.74 -983.0483 121.4 b8/-0.46 -984.4747 78.9 ? -1041.6875 69.5 a9/-0.86 -1053.0312 151.3 b9-17/-0.48,b9-18/0.50 -1071.0249 142.3 b9/0.49,y9-102/-0.19 -1084.5024 69.5 y8-18/-0.06 -1102.9705 204.8 y8/0.39 - -Name: AC[339]EPGVDYVYK/2 -LibID: 1 -MW: 1480.7308 -PrecursorMZ: 740.3654 -Status: Normal -FullName: X.AC[339]EPGVDYVYK.X/2 (CID) -Comment: AvePrecursorMz=740.8029 BestRawSpectrum=serum33.01694.01694 BinaryFileOffset=22975 CollisionEnergy=0.0 ConsFracAssignedPeaks=0.558 DotConsensus=0.87,0.05;0/3 FracUnassigned=0.08,1/5;0.13,4/20;0.18,120/267 Inst=1/UNKNOWN,3,0 MassDiff=0.5880 MassDiffCounts=2/1:2,2:1 MaxRepSN=35.0 Mods=1/1,C,ICAT-C:13C(9) NAA=11 NISTProtein=5/IPI00942927/IPI00783987/IPI00739237/ENSP00000245907/P01024 NMC=0 NTT=1 Nreps=3/3 OrigMaxIntensity=1.1e+07 Parent=740.365 Pep=Tryptic PrecursorIntensity=2.2e+07 Prob=1.0000 ProbRange=1,1,1,1 Protein=1/5/IPI00942927/IPI00783987/IPI00739237/ENSP00000245907/P01024 RepFracAssignedPeaks=0.479 RepNumPeaks=322.0/50.0 RetentionTime=3645.5,3742.0,3558.6 SN=200.0 Sample=1/PID_serum,3,3 Se=1^K3:ex=0.7447/0.6316,fv=3.0427/1.0635,hs=415.0000/38.8416,ns=331.0000/34.3220,pb=0.9998/0.0000 Spec=Consensus TotalIonCurrent=7.3e+07 -NumPeaks: 138 -235.0462 72.1 ? 2/2 0.0133|0.21 -241.1619 72.6 ? 2/2 0.0438|0.63 -252.0775 153.2 ? 2/2 0.0640|0.18 -253.0194 104.5 b3-35^2/-0.09 2/2 0.0484|0.35 -254.1315 350.1 ? 3/2 0.0501|0.52 -270.1049 1946.0 b3^2/-0.53,y4-35^2/0.97 3/2 0.0524|0.34 -271.0939 253.7 ? 3/2 0.0734|0.36 -272.0813 182.4 ? 2/2 0.0361|0.60 -274.2663 188.3 y2-35/-0.87 2/2 0.0352|0.11 -277.0917 202.1 ? 3/2 0.2194|0.57 -278.0872 708.7 y4-17^2/-0.06,y4-18^2/0.43 3/2 0.0614|0.23 -292.1574 99.7 y2-18/-0.01,y2-17/-0.99 2/2 0.0057|0.11 -295.0287 118.3 ? 2/2 0.1028|0.40 -296.1373 204.7 b4-46^2/-0.02,b5-102^2/-0.33 2/2 0.0482|0.26 -310.0700 362.7 y2/-0.11,b4-17^2/-0.57,b4-18^2/-0.08 2/2 0.0436|0.64 -321.8962 44.2 y5-44^2/-0.28,y5-46^2/0.73 2/2 0.0430|0.25 -323.0528 111.1 ? 2/2 0.0182|0.00 -325.1004 1177.5 b5-46^2/0.44,b5-44^2/-0.57 3/2 0.0801|0.61 -331.9786 175.8 ? 2/2 0.0145|0.78 -348.3743 188.2 b5^2/0.71 2/2 0.0532|0.44 -349.1990 1422.5 ? 3/2 0.0246|0.42 -350.1729 168.9 ? 3/2 0.0654|0.23 -351.2245 149.0 ? 2/2 0.0354|0.17 -361.1144 155.2 ? 2/2 0.0355|0.26 -366.0603 826.8 y3-44/0.81 2/2 0.0935|0.20 -369.1060 180.4 ? 2/2 0.0131|0.40 -376.2592 158.5 y6-35^2/0.07,y6-36^2/0.56 2/2 0.0648|0.45 -377.0597 605.8 ? 3/2 0.0512|0.29 -377.9969 144.0 ? 3/2 0.0298|0.45 -383.1463 73.7 a2/-0.07,a6^2/-0.06 2/2 0.0322|0.06 -394.0596 1671.2 y6^2/0.35,b2-17/-0.12 3/2 0.0575|0.41 -395.1213 441.6 b2-17i/-0.06 3/2 0.0087|0.69 -409.4444 231.8 y3/0.20 2/2 0.1247|0.35 -411.0866 617.9 b2/-0.12 3/2 0.1107|0.54 -412.1729 645.7 b2i/-0.04 2/2 0.0202|0.98 -424.2558 34.9 ? 2/2 0.0382|0.51 -427.1331 41.8 ? 2/2 0.0000|0.31 -436.2637 55.3 ? 3/2 0.0417|0.21 -437.1697 221.2 b7-35^2/-0.03,b3-102/-0.68,b7-36^2/0.47 2/2 0.0357|0.67 -439.1306 49.5 ? 2/2 0.0421|0.16 -451.2655 90.9 ? 3/2 0.0781|0.23 -460.0024 169.6 ? 2/2 0.0673|0.25 -461.2011 50.9 ? 2/2 0.0280|0.23 -461.9786 141.9 y8-18^2/0.24,y8-17^2/-0.25 2/2 0.0455|0.39 -479.7584 206.7 ? 2/2 0.2260|0.24 -495.1992 142.1 b3-46/0.95 2/2 0.0119|0.50 -498.2416 80.4 ? 3/2 0.0059|0.12 -505.0964 558.5 b3-35/-0.12 2/2 0.0338|0.61 -523.1347 709.1 b3-17/-0.09,b3-18/0.89,a8^2/0.89,b9-127^2/0.85 3/2 0.1245|0.42 -524.0770 188.5 b3-17i/-0.15 2/2 0.0967|0.17 -540.5306 1969.4 b3/0.28 3/2 0.4416|0.22 -542.1607 327.5 ? 2/2 0.1283|0.19 -543.2068 138.9 ? 2/2 0.1939|0.00 -551.1218 207.4 ? 2/2 0.0144|0.67 -553.3998 333.1 ? 3/2 0.1828|0.91 -554.4981 204.3 y4-18/0.20,y4-17/-0.78 3/2 0.0589|0.41 -566.2311 144.0 ? 2/2 0.2555|0.15 -569.2279 59.9 b9-35^2/0.97 2/2 0.0288|0.74 -572.2041 1094.3 y4/-0.10,a9^2/0.42 3/2 0.0158|0.14 -573.2835 357.2 y4i/-0.02 3/2 0.1143|0.31 -574.2922 105.8 y4i/-0.02 2/2 0.0237|0.03 -582.1698 156.2 ? 2/2 0.1001|0.00 -586.2241 131.8 b9^2/0.44 2/2 0.0101|0.74 -597.3989 93.0 ? 2/2 0.0172|0.98 -612.3705 222.5 ? 2/2 0.0359|0.58 -622.1605 137.7 ? 2/2 0.0097|0.43 -631.3537 258.3 ? 3/2 0.0443|0.41 -632.2229 211.8 ? 2/2 0.0502|0.11 -634.2368 242.8 ? 2/2 0.0188|0.58 -644.9899 126.6 b10-44^2/-0.33,b10-46^2/0.68 2/2 0.0057|0.16 -654.3123 141.0 y10-102^2/0.67,a10^2/1.00 2/2 0.0266|0.55 -658.2453 407.2 b10-18^2/-0.06,b10-17^2/-0.55 2/2 0.1232|0.56 -670.7037 278.5 y5-17/0.40 2/2 0.1262|0.65 -674.2417 48.8 ? 2/2 0.0391|0.19 -677.6740 105.1 p-127^2/0.81,b5-17/0.37 2/2 0.0171|0.35 -679.9149 318.3 ? 2/2 0.2670|0.21 -687.2676 1071.1 y5/-0.07,y10-35^2/-0.06,y10-36^2/0.43 3/2 0.1089|0.12 -688.1693 216.7 y5i/-0.17 3/2 0.0413|0.47 -688.9847 2187.8 p-102^2/-0.18,y5i/-0.35 3/2 0.1097|0.21 -689.8105 512.3 ? 3/2 0.2963|0.55 -690.2487 393.5 b6-102/-0.75 2/2 0.1962|0.83 -695.2369 84.0 b5/0.91,y10-18^2/-0.60 2/2 0.0281|0.23 -697.2747 259.4 y10-17^2/0.94 2/2 0.0821|0.65 -698.2923 152.9 ? 2/2 0.0051|0.12 -705.2181 554.9 y10^2/0.37 3/2 0.2847|0.33 -706.0849 275.4 ? 2/2 0.0143|0.09 -714.0747 219.5 ? 2/2 0.2184|0.39 -721.6040 521.6 ? 2/2 0.1928|0.20 -722.6562 332.3 p-35^2/-0.19,p-36^2/0.30 3/2 0.3124|0.67 -723.3418 260.8 p-35^2i/-0.01 2/2 0.1067|0.31 -730.6774 438.9 ? 3/2 0.2333|0.78 -731.6562 623.3 p-17^2/-0.20,p-18^2/0.30 2/2 0.1498|0.14 -733.1946 187.9 ? 2/2 0.0742|0.23 -739.2455 317.1 ? 3/2 0.0125|0.79 -748.3103 214.3 b6-46/0.92 2/2 0.0042|0.04 -760.0866 110.5 ? 2/2 0.0381|0.25 -775.2327 247.5 b6-18/-0.15 2/2 0.0120|0.41 -776.3476 359.4 b6-17/-0.02 2/2 0.1624|0.12 -777.1972 133.4 b6-17i/-0.17 2/2 0.0000|0.37 -786.2080 219.7 y6/-0.20 3/2 0.0775|0.42 -787.3005 202.3 y6i/-0.10 2/2 0.0313|0.26 -794.2209 216.6 b6/0.82 3/2 0.0699|0.52 -795.2630 140.1 b6i/0.87 2/2 0.0250|0.35 -812.0685 260.1 ? 3/2 0.1101|0.11 -813.1313 162.0 ? 2/2 0.0511|0.72 -814.5082 75.0 ? 2/2 0.0246|0.28 -843.3935 306.1 y7/-0.03 3/2 0.0292|0.43 -844.2050 184.0 y7i/-0.22 2/2 0.1387|0.41 -891.4008 141.6 b7-17/0.00,b7-18/0.99 3/2 0.0535|0.31 -895.1919 215.0 y8-46/0.72 2/2 0.2838|0.24 -900.1415 101.7 ? 2/2 0.0232|0.81 -908.4444 428.6 b7/0.02 3/2 0.2141|0.44 -909.3757 277.7 b7i/-0.05 3/2 0.0644|0.50 -922.4430 297.6 y8-18/-0.02 3/2 0.0648|0.25 -923.3659 157.8 y8-17/-0.09 3/2 0.1067|0.28 -939.7819 660.7 ? 2/2 0.0084|0.52 -940.3979 10000.0 y8/-0.08 3/2 0.0244|0.00 -941.4274 5759.2 y8i/-0.05 3/2 0.0237|0.23 -942.4104 1021.7 y8i/-0.07 3/2 0.0453|0.07 -943.4886 125.9 b8-127/-1.00 2/2 0.0039|0.03 -975.2937 70.9 ? 2/2 0.0254|0.17 -1051.3158 1102.5 y9-18/-0.19 3/2 0.0272|0.10 -1052.3299 287.6 y9-17/-0.16 3/2 0.0693|0.18 -1069.3931 2268.5 y9/-0.13 3/2 0.0253|0.18 -1070.3835 1310.1 y9i/-0.14 3/2 0.0662|0.06 -1071.4104 534.8 y9i/-0.11,b8/-0.08 3/2 0.1490|0.34 -1072.3665 304.4 b8i/-0.12 2/2 0.0462|0.09 -1089.2654 133.2 ? 2/2 0.0190|0.54 -1128.4901 176.2 ? 2/2 0.1331|0.59 -1129.3238 163.7 ? 2/2 0.0082|1.01 -1155.5561 56.4 ? 2/2 0.0449|0.33 -1170.3649 322.3 b9/-0.19 2/2 0.1138|0.06 -1171.3276 566.3 b9i/-0.23 2/2 0.2057|0.70 -1172.5512 230.7 b9i/-0.00 2/2 0.0051|0.43 -1192.4395 125.4 ? 2/2 0.0385|0.23 -1230.3553 96.3 b10-102/-0.86 2/2 0.0295|0.17 -1232.4228 160.4 ? 2/2 0.1749|0.33 -1334.5236 103.3 b10/0.91 2/2 0.0582|0.63 - -Name: AC[339]EPGVDYVYK/3 -LibID: 2 -MW: 1481.7381 -PrecursorMZ: 493.9127 -Status: Normal -FullName: X.AC[339]EPGVDYVYK.X/3 (CID) -Comment: AvePrecursorMz=494.2044 BinaryFileOffset=29662 CollisionEnergy=0.0 FracUnassigned=0.18,1/5;0.35,9/20;0.20,43/132 Inst=1/UNKNOWN,1 MassDiff=0.5600 Mods=1/1,C,ICAT-C:13C(9) NAA=11 NISTProtein=5/IPI00942927/IPI00783987/IPI00739237/ENSP00000245907/P01024 NMC=0 NTT=1 Nreps=1/1 OrigMaxIntensity=1.3e+05 Parent=493.913 Pep=Tryptic PrecursorIntensity=8.7e+06 Prob=1.0000 Protein=1/5/IPI00942927/IPI00783987/IPI00739237/ENSP00000245907/P01024 RawSpectrum=serum33.01704.01704 RetentionTime=3575.3,3575.3,3575.3 Sample=1/PID_serum,1,1 Se=1^K1:pb=0.9998/0,fv=2.3354/0,hs=441/0,ns=366/0,ex=0.8600/0 Spec=Single TotalIonCurrent=1.8e+06 -NumPeaks: 132 -166.9577 1082.5 b3-44^3/0.87 -176.8849 671.6 y4-44^3/0.11,y4-46^3/0.78 -182.9951 702.0 y3-44^2/-0.14,y3-46^2/0.87 -197.0587 934.1 y3-17^2/0.45,y3-18^2/0.94,b2-17^2/-0.54,b4-46^3/-0.71,b5-102^3/-0.92 -209.1381 650.4 ? -211.1024 587.5 ? -222.8289 142.4 y5-18^3/-0.95,a5^3/0.05,b6-127^3/0.03 -240.5461 257.2 ? -245.2284 350.6 ? -246.7267 1012.6 y6-46^3/-0.74,b3-46^2/-0.90 -249.7553 115.5 b6-46^3/-0.05,b6-44^3/-0.72 -253.8956 763.5 b6-35^3/0.44,b3-35^2/0.78 -263.2322 330.0 y6^3/0.43,y2-46/-0.94,y4-46^2/-0.42 -265.2750 106.5 b6^3/0.14,y2-44/-0.91,y4-44^2/0.61 -268.8241 827.4 y4-35^2/-0.31,b4-102^2/0.87,b7-102^3/-0.52,y7-36^3/-0.98 -272.0803 887.7 ? -281.2155 135.6 y7^3/-0.60 -289.1541 697.1 b7-44^3/0.34 -292.0881 215.4 y2-18/-0.08,b7-35^3/0.29,b7-36^3/0.62 -304.2629 511.7 b7^3/0.78,a4^2/-0.90 -307.3214 1014.7 y8-18^3/-0.84 -310.0618 2970.8 y2/-0.11,b4-17^2/-0.58,b4-18^2/-0.09 -312.2454 536.9 ? -319.1427 259.5 b4^2/-0.01 -321.1188 839.1 y5-46^2/-0.05 -323.2678 1225.2 b8-102^3/-0.43 -329.0795 264.3 ? -330.4944 922.8 b5-35^2/0.35 -333.8099 451.8 b6-127^2/0.11,a5^2/0.14 -335.0503 1553.6 y5-18^2/-0.12,y5-17^2/-0.61 -347.4829 447.9 b5^2/-0.18 -350.2500 746.1 y9-18^3/-0.92 -353.1027 446.7 b8-17^3/0.94 -359.1492 279.5 ? -359.9015 222.8 ? -364.7015 439.5 y3-44/-0.55 -366.0850 511.0 ? -367.8979 338.9 ? -368.8140 954.4 ? -369.8367 1054.0 y6-46^2/-0.87 -371.2726 197.2 ? -372.4462 2233.9 y6-44^2/0.74 -379.7695 947.6 b6-35^2/0.09,b9-35^3/0.59,b9-36^3/0.92 -380.7637 2990.9 a9^3/-0.76 -381.4627 485.0 ? -382.8998 4868.6 a2/-0.32,a6^2/-0.30 -387.7991 2499.0 b6-18^2/-0.40,b6-17^2/-0.89 -391.4217 1008.5 y3-18/0.19,y3-17/-0.80,b9^3/0.57,b7-127^2/0.21 -397.3707 3607.5 b6^2/0.17 -398.0167 0.6 ? -403.2952 1484.9 b7-102^2/-0.22,y7-36^2/-0.91,b10-127^3/0.42 -405.9086 87.7 ? -406.8494 572.1 ? -407.8199 788.7 ? -409.5999 398.8 y3/0.36 -411.3236 203.9 b2/0.11,b10-102^3/0.25 -411.9911 428.4 ? -418.5608 699.4 ? -421.0281 665.5 ? -422.1254 695.5 y7^2/-0.09 -422.8133 471.5 y7^2i/0.10 -423.4333 0.2 ? -425.9720 1663.6 ? -428.0353 3831.2 y10-127^3/0.13 -429.3826 254.2 b10-46^3/-0.49 -435.3969 503.4 a10^3/-0.48 -436.2788 354.4 y10-102^3/0.18,b7-36^2/-0.43,b7-35^2/-0.92 -439.0101 309.0 b10-18^3/-0.20,b10-17^3/-0.53 -443.9985 1198.0 ? -444.7723 543.5 b10^3/-0.44 -446.1472 1450.5 b7-17^2/-0.05,b7-18^2/0.44 -448.2025 3955.2 y8-46^2/0.46,y8-44^2/-0.54 -448.9516 345.4 y8-44^2i/-0.30 -454.9142 3546.6 b7^2/0.20,y10-44^3/-0.66,y10-46^3/0.02 -455.5296 1.4 b7^2i/0.31 -461.2227 255.2 y8-18^2/-0.51 -465.3459 894.3 y10-17^3/0.79 -470.8877 4777.7 y8^2/0.15,y10^3/0.65 -471.6147 0.7 ? -472.7448 1135.4 b8-127^2/-0.00 -475.9171 1028.9 ? -478.2982 1466.0 p-46^3/-0.28 -479.3643 802.0 p-44^3/0.11 -484.1340 1855.5 b8-102^2/-0.91 -485.8842 393.5 ? -489.0222 995.7 p-17^3/0.79 -493.9097 191.3 p^3/-0.00,b3-46/-0.34 -495.3246 482.4 b3-44/-0.94 -501.2201 1393.4 ? -508.3822 1191.3 ? -512.2888 973.3 a3/0.03,b8-46^2/-0.96,y9-44^2/-0.98,y9-46^2/0.03 -522.2363 1550.1 b3-18/-0.01,a8^2/-0.01,b9-127^2/-0.04 -523.0604 558.4 b3-17/-0.17 -524.0551 2254.0 b3-17i/-0.17 -526.4175 1786.7 y9-18^2/0.16,y9-17^2/-0.33,b8-18^2/-0.82,y4-46/0.12 -534.4785 244.8 b9-102^2/-0.10,b4-102/-0.43 -536.1433 541.1 y9^2/0.88,b8^2/-0.10 -540.1621 725.9 b3/-0.09 -541.1672 891.0 b3i/-0.09 -548.4319 1505.7 ? -566.1096 628.8 ? -567.0170 393.1 b5-127/-0.31,b9-36^2/-0.75 -571.0602 1369.1 [a9^2/-0.7233] -572.2891 2637.2 y4/-0.02,a9^2/0.51 -586.2849 507.0 b9^2/0.50 -588.0881 136.0 ? -600.2826 801.0 ? -603.2690 516.9 b10-127^2/-0.54,b4-35/1.00 -606.3643 187.5 ? -611.9160 75.3 ? -637.0220 522.7 b4/-0.28 -653.1891 294.8 a10^2/-0.13,y5-35/0.89,y10-102^2/-0.46 -666.2354 552.7 a5/-0.10,b6-127/-0.16 -676.4266 342.2 b10+18^2/0.11,b5-18/0.11,b5-17/-0.87 -683.9277 194.8 ? -687.3077 10000.0 y5/-0.03,y10-35^2/-0.02,y10-36^2/0.47 -688.2158 1409.0 y5i/-0.12 -693.1113 1532.5 ? -694.0155 4911.5 b5/-0.31 -695.0273 3030.5 b5i/-0.30,y10-18^2/-0.81 -739.5100 637.5 y6-46/-0.89 -744.5304 914.4 ? -756.3082 827.5 ? -774.0411 1340.1 ? -780.3457 363.0 ? -786.3558 902.7 y6/-0.05 -806.0834 262.9 b7-102/0.06 -821.5615 2407.8 ? -844.1727 1415.2 y7/0.75 -907.7101 1418.8 b7/-0.71 -915.1899 559.4 ? -940.3259 651.8 y8/-0.15 - diff --git a/implementations/python/examples/chinese_hamster_hcd_selected_head.msp b/implementations/python/examples/chinese_hamster_hcd_selected_head.msp deleted file mode 100644 index bb58110..0000000 --- a/implementations/python/examples/chinese_hamster_hcd_selected_head.msp +++ /dev/null @@ -1,1000 +0,0 @@ -Name: AAAACALTPGPLADLAAR/2_1(4,C,CAM)_46eV -MW: 1710.9076 -Comment: Single Pep=Tryptic Mods=1(4,C,CAM) Fullname=R.AAAACALTPGPLADLAAR.L Charge=2 Parent=855.4538 Se=1(^G1:sc=8.13346e-015) Mz_diff=1.4ppm HCD=46eV Scan=5538 Origfile="CHO-K1_bRPLC_C1.RAW.FT.hcd.ch.MGF" Nreps=1/2 Sample="jhu_cho_brplc_cam" Protein="tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1" Unassign_all=0.2848 Unassigned=0.1879 max_unassigned_ab=0.45 num_unassigned_peaks=4/20 FTResolution=7500 ms2IsolationWidth=1.90 ms1PrecursorAb=8799173.32 Precursor1MaxAb=25273307.50 PrecursorMonoisoMZ=855.4550 Filter="FTMS + p NSI d Full ms2 855.96@hcd35.00 [140.00-1725.00]" -Num peaks: 87 -143.0823 14791.5 "b2/5.6ppm" -153.2575 5008.6 "?" -159.0917 11531.8 "?" -162.5977 5804.6 "?" -169.0972 12931 "?" -175.1193 18211.1 "y1/2.0ppm,IRJ/2.0ppm" -194.0699 6011 "?" -199.1074 6737.4 "?" -201.7527 5576.3 "?" -212.1051 13786.1 "?" -214.1195 82269.8 "b3/4.1ppm" -229.1552 7852 "?" -232.0764 28555.9 "?" -249.1071 4670.7 "?" -257.1633 15001.9 "a4/9.7ppm" -276.4497 5288 "?" -283.1411 24965.9 "?" -283.3943 5090.5 "?" -285.1567 48285.5 "b4/3.4ppm" -302.1834 10558.9 "?" -303.114 52736.6 "?" -317.1891 6585.3 "y3/-12.9ppm" -345.1593 18050.6 "?" -354.1793 31400.1 "b5-NH2-CO-CH2SH/5.9ppm" -356.1916 7124.1 "?" -370.3776 6139.7 "?" -371.6662 11983.3 "?" -374.1505 34930.7 "?" -416.2029 8953.6 "?" -417.1931 16940.5 "a5/3.9ppm" -425.2171 15449.8 "b6-NH2-CO-CH2SH/6.6ppm" -428.2024 8874.5 "Int/cALT-H2O/14.4ppm" -428.249 6831.1 "?" -430.278 30118.6 "y4/1.8ppm" -445.1886 57883.2 "b5/5.0ppm" -446.2049 8868.2 "Int/cALT/-4.2ppm" -457.1753 5403.5 "?" -467.2682 6117.4 "?" -469.2735 6906.4 "?" -471.2018 9435.3 "?" -487.2299 15480.3 "?" -488.2367 13813.7 "a6/16.6ppm" -490.7795 12739.9 "y10^2/-0.6ppm" -491.2839 6651 "y10^2+i/5.4ppm" -495.9153 6370.5 "?" -499.2364 5273.9 "Int/AcALT-H2O/6.2ppm" -516.2236 49862.4 "b6/0.2ppm" -528.2323 9881.3 "?" -530.2752 10333.1 "?" -541.3164 7041.3 "?" -545.308 6833.8 "y5/7.0ppm" -558.2726 23958.7 "?" -570.3232 6006.3 "?" -601.3148 11919.6 "a7/3.6ppm" -617.2834 5841.2 "?" -617.3372 4342.1 "?" -629.3052 22419.3 "b7/-3.7ppm" -641.3058 11147.2 "Int/AAAcALT-H2O/-2.7ppm" -659.3259 9164.2 "Int/AAAcALT/11.8ppm" -685.3383 6861 "?" -712.3472 13798.2 "b8-H2O/3.6ppm" -730.3578 16426.3 "b8/3.5ppm" -826.4765 18892.5 "y8/-2.0ppm" -855.017 7062.7 "?" -855.5167 249849 "?" -856.523 57946.3 "?" -883.4993 29383.7 "y9/-0.3ppm" -922.4447 6413.2 "?" -934.4906 6605.4 "?" -963.5431 13545.1 "y10-NH3/17.9ppm" -980.556 559065 "y10/3.7ppm" -981.5587 216762 "y10+i/3.6ppm" -1037.5859 14218.2 "?" -1038.5812 9574.2 "?" -1067.8983 6611.6 "?" -1081.6041 179858 "y11/3.8ppm" -1082.6077 79540.9 "y11+i/4.5ppm" -1143.0283 6099.8 "?" -1194.6899 106907 "y12/4.9ppm" -1195.6869 50339.1 "y12+i/-0.1ppm" -1265.7273 83029.7 "y13/4.8ppm" -1266.7281 42164.7 "y13+i/3.2ppm" -1390.1328 5531.5 "?" -1395.6904 8549.2 "?" -1425.7538 51400.1 "y14/1.4ppm" -1426.7601 40643.8 "y14+i/3.8ppm" -1496.7792 11918.3 "y15/-6.5ppm" - -Name: AAAACALTPGPLADLAAR/2_1(4,C,CAM)_53eV -MW: 1710.9076 -Comment: Single Pep=Tryptic Mods=1(4,C,CAM) Fullname=R.AAAACALTPGPLADLAAR.L Charge=2 Parent=855.4538 Se=1(^G1:sc=1.31932e-020) Mz_diff=4.2ppm HCD=53eV Scan=6275 Origfile="RO-QC-141112_Betenbaugh_HK_Fraction46.raw.FT.hcd.ch.MGF" Nreps=1/14 Sample="betenbaugh_hk2" Protein="tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1" Unassign_all=0.3165 Unassigned=0.1420 max_unassigned_ab=0.16 num_unassigned_peaks=5/20 FTResolution=15000 ms2IsolationWidth=1.90 ms1PrecursorAb=1776618.56 Precursor1MaxAb=12167259.65 PrecursorMonoisoMZ=855.4574 Filter="FTMS + p NSI d Full ms2 855.95@hcd35.00 [140.00-1725.00]" -Num peaks: 204 -143.0814 9555.6 "b2/-0.7ppm" -169.097 5174.5 "?" -171.1126 2428.2 "?" -175.1069 1175.7 "?" -175.1187 7806.9 "y1/-1.4ppm,IRJ/-1.4ppm" -178.0645 645.1 "?" -181.0971 2623.7 "?" -183.1495 1770.8 "Int/PL-CO/1.7ppm" -185.0921 4004 "?" -185.1288 983.4 "Int/LA/1.9ppm" -199.1073 2854.3 "?" -203.1022 2225.3 "?" -203.412 489.7 "?" -204.0803 4532 "?" -211.1438 1671.5 "Int/PL/-1.4ppm" -212.103 6959.1 "y2-2NH3/0.2ppm" -214.1185 23984.8 "b3/-0.5ppm" -215.0481 1035.3 "?" -215.1219 1943.5 "b3+i/2.3ppm" -215.1392 1652.7 "Int/LT/0.8ppm" -216.0967 632.6 "?" -229.1299 970.3 "y2-NH3/1.7ppm" -231.1446 601.8 "?" -232.0748 11826.6 "?" -235.1929 547.3 "?" -240.1344 3195.6 "?" -242.1137 1025.5 "?" -246.1558 1514.8 "y2/-1.1ppm" -255.1454 790.9 "?" -256.1652 1376.9 "?" -257.1605 3523.6 "a4/-1.2ppm" -258.0901 1119.1 "?" -268.1656 1623.7 "Int/ALT-H2O/0.1ppm" -282.1807 1542.2 "Int/PLA/-1.8ppm" -283.14 10639.1 "?" -284.1443 1021 "?" -285.1555 11955.3 "b4/-0.8ppm" -286.1599 1072.8 "b4+i/4.8ppm" -286.1761 2533.2 "Int/ALT/-0.1ppm" -293.366 528.7 "?" -298.177 1429.9 "?" -302.1818 2634.5 "?" -303.1121 15782.5 "?" -304.1151 1344.9 "?" -309.1558 945 "?" -311.1712 2335.2 "?" -317.1934 2115 "y3/0.7ppm" -327.2036 961.2 "?" -328.1647 1131.6 "?" -329.1273 3077.6 "?" -331.1088 859.4 "?" -337.2232 2252 "Int/PGPL-CO/-0.6ppm" -339.2033 1220.8 "?" -341.1834 794.7 "?" -345.1589 6582.2 "?" -346.1541 1361.2 "?" -353.2189 1800 "?" -354.1769 9317.5 "b5-NH2-CO-CH2SH/-0.8ppm" -355.1793 1293.7 "b5-NH2-CO-CH2SH+i/-1.9ppm" -356.1933 1800.3 "?" -357.211 686.5 "?" -358.2065 618.4 "?" -363.3883 563.8 "?" -365.2181 2776.2 "y7^2/4.9ppm" -366.2212 705.5 "?" -368.1942 682 "?" -369.3904 685.6 "?" -370.4914 4171.5 "?" -372.1714 835.1 "?" -374.149 10475.6 "?" -375.153 1112.5 "?" -380.1929 960.8 "?" -384.1859 584.6 "?" -386.2027 978.1 "?" -396.2243 975.1 "?" -397.2071 1560.8 "Int/PLAD/-2.7ppm" -398.2401 1130.2 "?" -400.1644 4875.2 "?" -401.1676 730.6 "?" -402.1434 1170.3 "?" -408.2588 885.8 "Int/PGPLA-CO/-4.2ppm" -410.2415 678.5 "?" -416.1944 2264.1 "?" -417.192 3203.6 "a5/1.3ppm" -418.1938 714.5 "a5+i/-0.6ppm" -422.2396 762.6 "?" -425.2144 2490.8 "b6-NH2-CO-CH2SH/0.2ppm" -428.1953 1647.7 "Int/cALT-H2O/-2.1ppm" -430.2767 20600 "y4/-1.3ppm" -431.2812 3236 "y4+i/2.9ppm" -436.2548 3128.6 "Int/PGPLA/-1.5ppm" -442.2117 1223.9 "?" -445.1862 10843.9 "b5/-0.4ppm" -446.1865 1519 "b5+i/-5.6ppm" -446.2101 1269.8 "Int/cALT/7.4ppm" -454.23 854.8 "?" -459.2378 1549.6 "?" -471.2021 2150.3 "?" -473.1871 733.9 "?" -474.2351 776.1 "?" -487.2318 3002.2 "?" -488.2279 2861.1 "a6/-1.4ppm" -490.7802 1998.5 "y10^2/0.8ppm" -493.2748 802.6 "?" -499.2884 798.8 "?" -505.2755 1577.1 "?" -513.2489 2142.4 "?" -516.223 7108.2 "b6/-1.0ppm" -517.22 1175.7 "b6+i/-11.9ppm" -528.2206 1033.3 "?" -528.2757 1044.1 "y5-NH3/-3.7ppm" -530.2791 1202.4 "?" -533.272 1261.5 "?" -535.1867 572.4 "?" -543.2589 744.4 "?" -545.3041 3290.4 "y5/-0.2ppm" -546.2418 626 "?" -546.3103 815.6 "y5+i/6.2ppm" -551.2829 4018.4 "Int/PGPLAD/0.9ppm" -552.287 815.2 "Int/PGPLAD+i/3.0ppm" -558.2695 4055.3 "?" -559.2736 821.5 "?" -570.2687 978.2 "Int/AAcALT-H2O/-3.1ppm" -588.277 1266.6 "Int/AAcALT/-6.8ppm" -601.3116 1037.7 "a7/-1.7ppm" -609.3334 1558.5 "?" -616.3435 2514.4 "y6/3.6ppm" -629.3079 1030.1 "b7/0.5ppm" -636.3726 1099.2 "Int/PGPLADL-CO/1.7ppm" -638.3498 623.7 "?" -641.3058 1372.7 "Int/AAAcALT-H2O/-2.7ppm" -659.3138 896.8 "Int/AAAcALT/-6.6ppm" -664.3644 2215.2 "Int/PGPLADL/-3.1ppm" -665.3702 616.9 "Int/PGPLADL+i/1.2ppm" -698.652 964.9 "?" -710.8712 676.6 "?" -712.343 766.7 "b8-H2O/-2.3ppm" -728.644 669.7 "?" -729.4229 1339.5 "y7/-3.4ppm" -730.3568 859 "b8/2.1ppm" -735.4047 1839.2 "Int/PGPLADLA/1.5ppm" -735.7518 597 "?" -736.4097 726.4 "b9-NH2-CO-CH2SH/14.8ppm,Int/PGPLADLA+i/4.3ppm" -758.5785 584.4 "?" -804.5634 599.5 "?" -806.4404 871.1 "Int/PGPLADLAA/-0.3ppm" -807.4396 706.8 "Int/PGPLADLAA+i/-5.0ppm" -809.4468 1047 "y8-NH3/-5.9ppm" -826.4767 5889.7 "y8/-1.7ppm" -827.4818 1704.1 "y8+i/1.0ppm" -835.4305 6503.5 "?" -836.4305 855.7 "?" -855.5272 1972.3 "?" -883.499 11027.3 "y9/-0.7ppm" -884.5011 4136.3 "y9+i/-1.5ppm" -920.521 899.9 "?" -922.4631 6661.9 "?" -923.4683 1004.4 "?" -938.5323 694.4 "?" -954.0876 657.8 "?" -962.5461 1056.8 "y10-H2O/4.5ppm" -963.5266 5559.2 "y10-NH3/0.8ppm" -964.5276 3037.9 "y10-NH3+i/-1.1ppm" -980.5516 101168 "y10/-0.8ppm" -981.5547 48825.1 "y10+i/-0.5ppm" -982.556 3169.3 "y10+2i/-1.8ppm" -998.153 653.4 "?" -1026.4183 641.1 "?" -1033.4918 1042.9 "?" -1037.5729 7440.8 "?" -1038.5754 4253.3 "?" -1050.5208 5312.6 "?" -1063.5883 1995.7 "y11-H2O/-1.1ppm" -1064.5804 1437.3 "y11-NH3/6.5ppm,y11-H2O+i/-11.2ppm" -1081.5985 28537.7 "y11/-1.4ppm" -1082.6017 16194.1 "y11+i/-1.1ppm" -1083.5983 1228.4 "y11+2i/-6.6ppm" -1150.6531 1305.7 "?" -1176.6824 1518.9 "y12-H2O/7.5ppm" -1177.6671 1170.1 "y12-NH3/8.1ppm,y12-H2O+i/-7.9ppm" -1182.254 639.1 "?" -1194.6826 20850.2 "y12/-1.3ppm" -1195.6853 12324.9 "y12+i/-1.4ppm" -1197.5858 4604.9 "?" -1221.6934 1065.9 "?" -1247.7007 1013.5 "y13-H2O/-8.0ppm" -1252.6328 702.9 "?" -1265.7198 16380.4 "y13/-1.1ppm" -1266.7246 9779.2 "y13+i/0.4ppm" -1267.7239 747.9 "y13+2i/-2.2ppm" -1298.6331 3899.6 "?" -1334.7629 576.6 "y14-NH2-CO-CH2SH/15.2ppm" -1395.6888 9418.6 "?" -1396.6947 2451.5 "?" -1407.7356 1083.1 "y14-H2O/-4.0ppm" -1408.7473 1011.7 "y14-NH3/15.6ppm,y14-H2O+i/2.3ppm" -1425.7515 7609.8 "y14/-0.3ppm" -1426.7562 7554 "y14+i/1.1ppm" -1466.0739 798.5 "?" -1495.1215 635.8 "?" -1496.7932 1534.6 "y15/2.8ppm" -1497.7944 1455 "y15+i/1.7ppm" -1557.3423 600.8 "?" -1628.3004 719.6 "?" - -Name: AAAAGQTGTVPPGAPGALPLPGMAIVK/2_0_76eV -MW: 2414.3344 -Comment: Single Pep=SemiTryptic Mods=0 Fullname=A.AAAAGQTGTVPPGAPGALPLPGMAIVK.E Charge=2 Parent=1207.1672 Se=1(^G1:sc=1.43642e-012) Mz_diff=-0.9ppm HCD=76eV Scan=7528 Origfile="RO-QC-141112_Betenbaugh_HK_Fraction18.raw.FT.hcd.ch.MGF" Nreps=1/2 Sample="betenbaugh_hk1" Protein="tr|G3I2Q7|G3I2Q7_CRIGR Transcription intermediary factor 1-beta OS=Cricetulus griseus GN=I79_017700 PE=4 SV=1" Unassign_all=0.2591 Unassigned=0.0000 max_unassigned_ab=0.12 num_unassigned_peaks=0/20 FTResolution=15000 ms2IsolationWidth=1.90 ms1PrecursorAb=6939079.20 Precursor1MaxAb=7583304.35 PrecursorMonoisoMZ=1207.1661 Filter="FTMS + p NSI d Full ms2 1207.67@hcd35.00 [140.00-2000.00]" -Num peaks: 122 -143.0816 2935.3 "b2/0.7ppm" -147.1127 2210.5 "y1/-0.7ppm" -154.4137 1587.1 "?" -155.0816 2825.2 "Int/PG/0.6ppm" -169.771 1665.2 "?" -176.5942 1535.3 "?" -181.0984 2034.3 "?" -186.0873 2509.4 "?" -198.5815 1458.2 "?" -199.2009 1692.3 "?" -206.924 1799.6 "?" -214.1185 6874.5 "b3/-0.5ppm" -214.6242 1695 "?" -216.197 1659.5 "?" -224.6321 1496.3 "?" -226.1183 6292.8 "Int/PGA/-1.4ppm" -227.4689 1609.1 "?" -230.1134 2157.9 "?" -240.1377 1613.7 "?" -246.1817 2500.8 "y2/2.0ppm" -252.1353 2976.9 "Int/PPG/4.1ppm" -257.1249 2901.5 "?" -257.1618 2468.8 "a4/3.8ppm" -266.3697 1813.9 "?" -283.6819 1747.3 "?" -285.1557 5707.9 "b4/-0.1ppm" -285.8154 1730.9 "?" -287.1343 2200.9 "?" -295.139 1768.2 "?" -295.1769 3116.9 "Int/PGAP-CO/1.5ppm,Int/PPGA-CO/1.5ppm" -323.1715 9768.4 "Int/PGAP/0.4ppm,Int/PPGA/0.4ppm" -326.1471 1541 "?" -328.1606 3372.4 "?" -339.2022 4142.5 "Int/PGAL/-1.4ppm" -342.1785 2123.8 "b5/3.8ppm" -357.1593 8559.3 "Int/PGMA/0.6ppm" -368.2019 1424.3 "?" -370.1709 2286.1 "?" -382.171 2478.3 "?" -399.199 2560.8 "?" -404.719 1744.2 "?" -411.2023 1764.9 "?" -412.2186 2214.1 "?" -416.1802 1569.1 "?" -425.2139 2586.2 "?" -427.1956 2391.1 "?" -436.2577 3485.4 "Int/PGALP/5.2ppm" -442.2464 3103.3 "a6/12.5ppm" -470.2405 9151 "b6/10.1ppm" -496.2594 3078.1 "Int/PLPGM/1.2ppm" -498.2301 3109 "?" -520.2899 2739.1 "Int/PPGAPGA-CO/4.0ppm" -526.2617 3852 "?" -539.2985 1828 "Int/PLPGMA-CO/-4.7ppm" -548.2831 5503.1 "Int/PPGAPGA/0.7ppm" -549.339 5105.4 "Int/PGALPL/-0.9ppm" -557.2015 1790.3 "?" -564.3132 2803.2 "Int/PGAPGAL/-1.5ppm" -564.4461 1473.4 "?" -567.2952 5860.9 "Int/PLPGMA/-1.3ppm" -569.3114 4720.3 "Int/PGMAIV/-0.3ppm" -571.2812 2601.4 "b7/-3.9ppm" -592.1807 1899.1 "?" -614.3491 1751.3 "?" -633.3705 7963.1 "Int/PGAPGALP-CO/-2.2ppm,Int/PPGAPGAL-CO/-2.2ppm" -640.3058 2814.4 "?" -661.3663 17369.3 "Int/PGAPGALP/-0.7ppm,Int/PPGAPGAL/-0.7ppm" -662.3647 3974.4 "Int/PGAPGALP+i/-7.5ppm,Int/PPGAPGAL+i/-7.5ppm" -680.3803 6159.2 "Int/PLPGMAI/0.5ppm" -687.8984 2815.3 "y15-NH3^2/5.9ppm" -695.8273 4004.9 "?" -699.8309 1878.5 "?" -706.7814 1733.4 "?" -711.3409 9244 "b9-H2O/-1.6ppm" -715.4171 25528.5 "y7/0.0ppm" -716.4193 6624.9 "y7+i/-0.9ppm" -720.4687 1548.7 "?" -740.657 1772 "?" -747.7864 1728.5 "?" -774.4467 2604 "Int/PGAPGALPL/-5.4ppm" -779.444 3102.9 "Int/PLPGMAIV/-5.7ppm" -792.3951 2288.2 "?" -792.5062 1866.9 "?" -793.287 2259.9 "?" -793.4606 4623.5 "y17^2/0.3ppm" -793.9547 2201.9 "y17^2+i/-9.0ppm" -843.5064 6631.8 "Int/PGAPGALPLP-CO/-2.7ppm,Int/PPGAPGALPL-CO/-2.7ppm" -871.5032 16269.2 "Int/PGAPGALPLP/-0.5ppm,Int/PPGAPGALPL/-0.5ppm" -872.5042 2808 "Int/PGAPGALPLP+i/-2.7ppm,Int/PPGAPGALPL+i/-2.7ppm" -905.4965 3245.9 "Int/PGALPLPGMA/5.7ppm" -925.5524 22654 "y9/-1.7ppm" -926.5582 6169.9 "y9+i/1.5ppm" -1025.5756 3014.9 "Int/PPGAPGALPLPG/-2.2ppm" -1038.6364 3465.3 "y10/-1.5ppm" -1050.3751 1648.4 "?" -1101.6609 1971.4 "?" -1156.626 2932.8 "Int/PPGAPGALPLPGM/6.6ppm" -1227.1982 1647 "?" -1227.6581 3903.5 "Int/PPGAPGALPLPGMA/2.2ppm" -1263.7479 15942.2 "y13/-1.1ppm" -1264.757 6224.1 "y13+i/3.8ppm" -1334.7977 1960.4 "y14/8.4ppm" -1340.7531 3560.4 "Int/PPGAPGALPLPGMAI/10.1ppm" -1356.4097 1828.1 "?" -1391.7969 3956.8 "y15/-7.9ppm" -1392.7919 2490.2 "y15+i/-13.6ppm" -1402.2483 2181.2 "?" -1466.1517 2524 "?" -1482.8165 2498.3 "?" -1488.8579 7946.7 "y16/-1.9ppm" -1489.8688 4824.6 "y16+i/3.5ppm" -1510.2008 2208.8 "?" -1511.4255 4721 "?" -1522.1158 2439.5 "?" -1554.3594 1714.9 "?" -1567.8997 3204.8 "y17-H2O/-2.0ppm" -1585.9117 37792.9 "y17/-1.1ppm" -1586.9141 23000.3 "y17+i/-1.4ppm" -1612.5677 1607.6 "?" -1616.5776 4065.9 "?" -1752.5294 2175.8 "?" -1980.9857 3567.9 "?" - -Name: AAAAGSTSVKPIFSR/2_0_44eV -MW: 1463.8086 -Comment: Single Pep=SemiTryptic Mods=0 Fullname=Q.AAAAGSTSVKPIFSR.D Charge=2 Parent=731.9043 Se=1(^G1:sc=6.33525e-018) Mz_diff=-2.7ppm HCD=44eV Scan=3052 Origfile="RO-QC-141112_Betenbaugh_HK_Fraction26.raw.FT.hcd.ch.MGF" Nreps=1/4 Sample="betenbaugh_hk4" Protein="tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1" Unassign_all=0.1681 Unassigned=0.0217 max_unassigned_ab=0.17 num_unassigned_peaks=1/20 FTResolution=15000 ms2IsolationWidth=1.90 ms1PrecursorAb=324419.29 Precursor1MaxAb=361702.23 PrecursorMonoisoMZ=731.9023 Filter="FTMS + p NSI d Full ms2 731.90@hcd34.00 [110.00-1475.00]" -Num peaks: 111 -110.1269 76.26 "?" -113.4028 68.16 "?" -115.0865 659.49 "a2/-0.8ppm" -129.1022 463.28 "IKD/-0.3ppm" -129.9147 62.91 "?" -129.9924 68.35 "?" -143.0815 2091.84 "b2/0.0ppm" -145.1529 69.39 "?" -167.7261 67.46 "?" -169.0972 508.54 "?" -175.1189 354.1 "y1/-0.3ppm,IKF/-0.3ppm,IRJ/-0.3ppm" -183.1488 80.6 "Int/PI-CO/-2.1ppm" -200.1034 223.41 "?" -214.1187 2461.15 "b3/0.4ppm" -215.1224 150.92 "b3+i/4.6ppm" -226.1194 166.15 "?" -228.0984 104.95 "?" -228.1709 81.16 "Int/VK/1.1ppm" -231.5444 76.88 "?" -240.136 109.39 "?" -242.1143 129.58 "?" -256.1299 117.54 "?" -257.1609 174.31 "a4/0.3ppm" -262.1501 113.33 "y2/-3.4ppm" -264.371 72.61 "?" -269.1243 138.11 "?" -270.1455 122.57 "?" -271.1404 453.74 "?" -281.1254 95.19 "?" -283.6823 109.92 "?" -285.1563 279.13 "b4/2.0ppm" -287.135 187.61 "?" -287.8068 65.78 "?" -297.1195 79.71 "?" -297.1555 129 "?" -299.1343 183.34 "?" -314.1814 114.14 "a5/-2.8ppm" -314.954 72.12 "?" -315.1298 108.82 "?" -342.1795 136.49 "b5/6.7ppm" -357.3935 72.21 "?" -358.2114 117.32 "Int/PIF/-3.1ppm" -370.173 101.69 "?" -374.2291 100.25 "y6^2/-0.3ppm" -384.186 84.78 "?" -390.441 73.17 "?" -392.1888 108.06 "y3-NH3/-10.3ppm" -409.2202 184.35 "y3/2.0ppm" -411.2 90.17 "b6-H2O/3.3ppm" -413.199 69.51 "?" -432.1567 69.03 "?" -457.2071 70.57 "?" -467.2223 88.32 "?" -467.28 113.01 "y8^2/1.2ppm" -469.7274 63.86 "?" -517.8033 126.12 "y9^2/0.0ppm" -522.3049 76.1 "y4/2.8ppm" -523.8322 67.7 "?" -551.1071 72.33 "?" -556.2686 106.48 "?" -561.3188 193.75 "y10^2/-0.9ppm" -561.8202 108.62 "y10^2+i/-1.0ppm" -589.8297 605.37 "y11^2/-0.6ppm" -590.3306 217.12 "y11^2+i/-1.5ppm" -602.33 179.57 "y5-NH3/0.5ppm" -613.2793 68.37 "?" -619.356 2943.26 "y5/-0.4ppm" -620.3603 685.92 "y5+i/1.9ppm" -625.349 501.99 "y12^2/0.7ppm" -625.8499 293.9 "y12^2+i/-0.2ppm" -626.1416 61.18 "?" -660.8675 419.89 "y13^2/0.5ppm" -661.3681 249.76 "y13^2+i/-0.7ppm" -667.6551 76.13 "?" -690.5546 80.2 "?" -691.2347 99.99 "?" -696.3888 148.08 "y14^2/4.4ppm" -696.8864 94.95 "y14^2+i/-1.1ppm" -699.1979 125.04 "?" -703.2349 88.5 "?" -707.3016 78.55 "?" -723.7889 71.89 "?" -730.4289 91.25 "y6-NH3/5.8ppm" -731.903 327.43 "p/-1.7ppm" -732.4063 260.03 "p+i/0.8ppm" -747.4508 1511.3 "y6/-0.5ppm" -748.4523 477.25 "y6+i/-2.3ppm" -813.9755 73.74 "?" -814.2291 68.08 "?" -846.5192 787.5 "y7/-0.5ppm" -847.5187 219.01 "y7+i/-4.5ppm" -933.5519 1204.76 "y8/0.3ppm" -934.5554 585.8 "y8+i/1.0ppm" -1034.5983 1246.92 "y9/-1.0ppm" -1035.6029 562.43 "y9+i/0.7ppm" -1043.6613 80.22 "?" -1078.0837 77.1 "?" -1121.6309 955.3 "y10/-0.4ppm" -1122.6306 445.79 "y10+i/-3.2ppm" -1160.6473 138.54 "y11-H2O/4.4ppm" -1161.6349 262.21 "y11-NH3/7.4ppm,y11-H2O+i/-8.8ppm" -1178.6521 2592.9 "y11/-0.6ppm" -1179.6555 1376.21 "y11+i/-0.1ppm" -1182.3555 67.85 "?" -1198.9932 63.25 "?" -1249.6902 1081.82 "y12/0.2ppm" -1250.691 611.72 "y12+i/-1.4ppm" -1320.7277 504.87 "y13/0.5ppm" -1321.7318 253.18 "y13+i/1.5ppm" -1389.0188 62.97 "?" -1465.9423 113.63 "?" - -Name: AAAAGSTSVKPIFSR/3_0_28eV -MW: 1464.8157 -Comment: Single Pep=SemiTryptic Mods=0 Fullname=Q.AAAAGSTSVKPIFSR.D Charge=3 Parent=488.2719 Se=1(^G1:sc=9.67069e-018) Mz_diff=3.8ppm HCD=28eV Scan=2890 Origfile="RO-QC-141112_Betenbaugh_HK_Fraction26.raw.FT.hcd.ch.MGF" Nreps=1/5 Sample="betenbaugh_hk3" Protein="tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1" Unassign_all=0.1804 Unassigned=0.0000 max_unassigned_ab=0.09 num_unassigned_peaks=0/20 FTResolution=15000 ms2IsolationWidth=1.90 ms1PrecursorAb=3390555.93 Precursor1MaxAb=3965011.86 PrecursorMonoisoMZ=488.2738 Filter="FTMS + p NSI d Full ms2 488.27@hcd34.00 [110.00-1475.00]" -Num peaks: 161 -110.4751 880.7 "?" -111.5315 809.7 "?" -112.087 1086.3 "IRG/0.7ppm" -115.0865 75818.4 "a2/-0.8ppm" -116.0703 1405.8 "IRI/-2.6ppm" -116.0899 1580.2 "a2+i/5.4ppm" -120.0808 2176.9 "IFA/0.2ppm" -129.0659 3793.3 "?" -129.1022 29530.7 "IKD/-0.3ppm" -130.1056 1054.6 "IKD+i/4.4ppm" -138.138 996.1 "?" -143.0815 89938.4 "b2/0.0ppm" -144.0849 3848.2 "b2+i/4.2ppm" -144.8468 964.9 "?" -145.0606 3718.8 "?" -153.0659 1282.7 "?" -158.0922 2201.6 "y1-NH3/-1.3ppm" -159.1125 2211.3 "?" -160.572 774.2 "?" -161.0918 1971.8 "?" -163.5364 927.8 "?" -169.0971 8412 "?" -171.0764 6416.5 "?" -175.1189 8291 "y1/-0.3ppm,IKF/-0.3ppm,IRJ/-0.3ppm" -177.5624 849.9 "?" -183.1492 2806.4 "Int/PI-CO/0.1ppm" -185.0934 958 "?" -189.0877 3809 "?" -198.0881 3160.3 "?" -200.103 8672.6 "?" -204.5067 880.9 "?" -210.0874 2471.9 "?" -211.1447 2133.4 "Int/PI/2.8ppm" -214.1187 22627.3 "b3/0.4ppm" -215.1205 976.2 "b3+i/-4.2ppm" -216.0981 4203.5 "?" -228.0981 5566.6 "y2-2NH3/1.0ppm" -228.1706 4194.9 "Int/VK/-0.2ppm" -240.0988 1395.3 "?" -240.1342 1105.3 "?" -242.1136 2814.5 "?" -244.1677 932.4 "?" -245.1246 2188.3 "y2-NH3/0.7ppm" -257.1618 1137.5 "a4/3.8ppm" -258.1086 4986.3 "?" -262.1516 3577 "y2/2.4ppm" -269.1245 3938.1 "?" -270.1448 3287.2 "?" -271.1396 2172.6 "?" -275.3359 1037 "?" -276.1198 996 "?" -276.2175 843.1 "?" -281.1246 2464.1 "?" -281.1612 873.4 "?" -285.157 1116.3 "b4/4.5ppm" -287.136 3444.7 "?" -297.1196 5420.4 "?" -299.1352 5315 "?" -310.1825 3745.4 "y5^2/2.4ppm" -315.1301 9824.1 "?" -323.1358 1153.1 "?" -333.1407 1547.3 "?" -339.168 816.3 "?" -352.1606 1609.5 "?" -357.1775 2103.4 "?" -365.7159 1399.2 "y6-NH3^2/-0.2ppm" -368.1564 3740.4 "?" -370.1726 2557.4 "?" -374.2292 5561.8 "y6^2/-0.1ppm" -374.7322 1301 "y6^2+i/4.1ppm" -376.1832 956.2 "?" -378.174 956.5 "?" -386.167 4098.3 "?" -386.2034 1795.4 "?" -392.193 3698 "y3-NH3/0.4ppm" -395.407 759.9 "?" -396.188 2827.1 "?" -404.1751 1611.3 "?" -404.2145 1149.9 "?" -409.2199 7096.2 "y3/1.2ppm" -414.1984 3857.6 "?" -420.7338 881.9 "?" -421.1867 1530.4 "?" -424.0701 904.3 "?" -439.1948 1910.9 "?" -440.9135 938 "y13^3/-0.8ppm" -457.2043 2679.7 "?" -467.2251 3238.5 "?" -467.2799 6142 "y8^2/1.0ppm" -467.7818 2674.9 "y8^2+i/1.9ppm" -485.2344 2370.1 "?" -508.7988 1318.3 "y9-H2O^2/1.6ppm" -517.804 8711.4 "y9^2/1.4ppm" -518.305 5346.7 "y9^2+i/0.5ppm" -520.2481 1151.1 "?" -522.3037 4970.1 "y4/0.5ppm" -534.7964 1651.3 "?" -538.2622 1220.7 "?" -552.317 2102.2 "y10-H2O^2/5.4ppm" -556.27 960.1 "?" -558.8151 1054.4 "?" -561.3193 9865.4 "y10^2/0.0ppm" -561.8219 3932.3 "y10^2+i/2.1ppm" -580.8237 4086.9 "y11-H2O^2/-1.8ppm" -581.3318 1582.3 "y11-H2O^2+i/9.7ppm" -589.8302 30985.9 "y11^2/0.3ppm" -590.3312 15287.5 "y11^2+i/-0.5ppm" -601.3485 2836 "y5-H2O/4.7ppm" -602.3292 3454.7 "y5-NH3/-0.8ppm" -603.3347 1573.2 "y5-NH3+i/3.5ppm" -604.2908 937.8 "?" -607.3416 3013 "?" -616.3441 2761.9 "y12-H2O^2/1.3ppm" -616.8438 2753.7 "y12-NH3^2/13.8ppm,y12-H2O^2+i/-1.5ppm" -617.736 1000.9 "?" -619.3562 112581 "y5/0.0ppm" -619.4061 1331.1 "?" -620.3597 26856.2 "y5+i/1.0ppm" -625.3489 29725.9 "y12^2/0.5ppm" -625.8499 17686.6 "y12^2+i/-0.2ppm" -651.8593 1435.9 "y13-H2O^2/-3.9ppm" -660.8666 17322.8 "y13^2/-0.8ppm" -661.3691 10845.8 "y13^2+i/0.8ppm" -665.7083 857.4 "?" -677.8406 865 "?" -679.6729 1028.1 "?" -692.6226 1839.8 "?" -696.39 1380.5 "y14^2/6.2ppm" -696.8853 1825.9 "y14^2+i/-2.6ppm" -712.8559 1575.5 "?" -729.4384 2131.4 "y6-H2O/-3.0ppm" -730.4251 3172.7 "y6-NH3/0.6ppm" -743.5792 878.1 "?" -747.4517 51670.9 "y6/0.7ppm" -748.454 16389.8 "y6+i/-0.1ppm" -846.519 23172.3 "y7/-0.7ppm" -847.5219 8878 "y7+i/-0.7ppm" -888.9458 1103 "?" -915.5491 1402.6 "y8-H2O/8.8ppm" -916.5312 1566.9 "y8-NH3/6.7ppm,y8-H2O+i/-13.9ppm" -933.5517 34961.3 "y8/0.1ppm" -934.5549 14638.2 "y8+i/0.4ppm" -962.5909 952.1 "?" -967.9422 926.5 "?" -1016.5936 1298.4 "y9-H2O/4.8ppm" -1017.5724 1109.4 "y9-NH3/-0.3ppm,y9-H2O+i/-18.9ppm" -1034.5992 17085.6 "y9/-0.1ppm" -1035.6008 7940 "y9+i/-1.3ppm" -1049.6464 924.5 "?" -1068.5891 1068.8 "?" -1072.3027 820.3 "?" -1100.4142 824.6 "?" -1121.6331 6228.7 "y10/1.6ppm" -1122.6238 3007.6 "y10+i/-9.3ppm" -1178.6527 11088.9 "y11/-0.1ppm" -1179.6552 6228.8 "y11+i/-0.4ppm" -1249.6901 2527.6 "y12/0.2ppm" -1250.6986 1715 "y12+i/4.7ppm" -1347.309 852.2 "?" -1465.9084 1527.1 "?" -1469.9915 925.5 "?" - -Name: AAAALGSHGSCSSEVEK/2_1(10,C,CAM)_50eV -MW: 1661.7668 -Comment: Single Pep=Tryptic Mods=1(10,C,CAM) Fullname=K.AAAALGSHGSCSSEVEK.E Charge=2 Parent=830.8834 Se=1(^G1:sc=6.94218e-013) Mz_diff=4.1ppm HCD=50eV Scan=1185 Origfile="RO-QC-141112_Betenbaugh_HK_Fraction18.raw.FT.hcd.ch.MGF" Nreps=1/2 Sample="betenbaugh_hk5" Protein="tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1" Unassign_all=0.4368 Unassigned=0.1840 max_unassigned_ab=0.45 num_unassigned_peaks=6/20 FTResolution=15000 ms2IsolationWidth=1.90 ms1PrecursorAb=30003.73 Precursor1MaxAb=28800.11 PrecursorMonoisoMZ=830.8868 Filter="FTMS + p NSI d Full ms2 831.38@hcd34.00 [110.00-1675.00]" -Num peaks: 68 -110.1102 57.808 "?" -115.0864 84.449 "a2/-1.6ppm" -128.1915 60.078 "?" -129.1023 157.87 "IKD/0.5ppm,y1-H2O/0.5ppm" -130.0863 143.466 "y1-NH3/0.4ppm" -134.6533 64.924 "?" -143.0814 409.786 "b2/-0.7ppm" -147.1131 319.305 "y1/2.0ppm" -151.4513 63.288 "?" -153.7949 64.094 "?" -159.3516 66.632 "?" -165.1407 62.763 "?" -185.7231 56.05 "?" -192.253 56.668 "?" -206.6181 58.523 "?" -207.8363 67.364 "?" -214.1188 604.289 "b3/0.9ppm" -240.1356 101.032 "?" -242.2549 68.729 "?" -252.7986 69.267 "?" -257.1606 92.981 "a4/-0.8ppm" -258.144 282.108 "y2-H2O/-3.2ppm" -276.1561 234.148 "y2/2.5ppm" -282.3431 71.242 "?" -285.1556 363.637 "b4/-0.5ppm" -312.7774 62.146 "?" -343.4806 65.426 "?" -355.0699 104.479 "?" -370.4347 269.799 "?" -375.2243 139.559 "y3/1.3ppm" -385.774 62.977 "?" -388.1424 58.351 "?" -431.0488 72.382 "?" -529.347 83.459 "?" -598.1849 62.213 "?" -688.806 84.319 "y13^2/-4.6ppm" -692.6966 113.075 "?" -694.6636 75.382 "?" -700.6682 128.47 "?" -725.4309 81.78 "?" -817.4878 85.857 "?" -819.1156 63.497 "?" -903.9632 63.514 "?" -982.4142 289.221 "y9/-0.4ppm" -983.42 122.064 "b11/-16.6ppm,y9+i/2.6ppm" -1036.3802 70.607 "?" -1104.5166 70.543 "?" -1119.4768 195.679 "y10/2.9ppm" -1120.4703 107.369 "y10+i/-5.3ppm" -1139.4911 84.154 "b13-H2O/1.1ppm" -1206.5106 83.121 "y11/4.2ppm" -1263.5344 229.989 "y12/5.9ppm" -1264.5262 152.204 "y12+i/-2.8ppm" -1268.5361 75.921 "b14-H2O/2.9ppm" -1286.5446 234.168 "b14/1.3ppm" -1287.5588 119.455 "b14+i/10.2ppm" -1376.6179 122.497 "y13/5.0ppm" -1376.9817 67.739 "?" -1451.4869 67.46 "?" -1465.7048 143.33 "?" -1480.5077 95.07 "?" -1522.3134 127.307 "?" -1554.5259 83.112 "?" -1595.7773 67.148 "?" -1608.2555 61.797 "?" -1623.9801 102.29 "?" -1628.4393 118.77 "?" -1670.2889 140.136 "?" - -Name: AAAALGSHGSCSSEVEK/2_1(10,C,CAM)_52eV -MW: 1661.7668 -Comment: Single Pep=Tryptic Mods=1(10,C,CAM) Fullname=K.AAAALGSHGSCSSEVEK.E Charge=2 Parent=830.8834 Se=1(^G1:sc=6.88234e-022) Mz_diff=-2.0ppm HCD=52eV Scan=868 Origfile="RO-QC-141112_Betenbaugh_HK_Fraction19.raw.FT.hcd.ch.MGF" Nreps=1/3 Sample="betenbaugh_hk2" Protein="tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1" Unassign_all=0.3390 Unassigned=0.0816 max_unassigned_ab=0.17 num_unassigned_peaks=3/20 FTResolution=15000 ms2IsolationWidth=1.90 ms1PrecursorAb=9544513.13 Precursor1MaxAb=26056925.91 PrecursorMonoisoMZ=830.8817 Filter="FTMS + p NSI d Full ms2 830.88@hcd35.00 [140.00-1675.00]" -Num peaks: 402 -141.1024 1824.4 "?" -143.0816 54472.6 "b2/0.7ppm" -144.0851 2028.2 "b2+i/5.6ppm" -147.1129 40570.6 "y1/0.7ppm" -148.1159 2104.9 "y1+i/1.9ppm" -151.6119 866.7 "?" -157.0613 1472.8 "Int/SS-H2O/3.4ppm" -157.0974 1742.9 "y1-H2O+CO/1.6ppm" -157.1335 2797.4 "?" -158.3324 771.5 "?" -158.4784 915 "?" -165.0449 784.1 "?" -169.0973 19654.9 "?" -170.1011 1507.2 "?" -170.2729 987 "?" -175.0683 1008.2 "Int/SS/-17.3ppm" -182.0172 1038.4 "?" -183.113 1337.8 "?" -183.1501 1174.6 "?" -185.1288 4333.2 "?" -195.0881 4158.9 "?" -196.1971 908.9 "?" -196.9482 1078.6 "?" -197.1034 2784.1 "?" -199.0719 3248 "?" -200.1024 1115.3 "?" -201.1237 7050.8 "?" -209.4671 931.3 "?" -211.1448 5058.2 "?" -213.1236 1676.9 "?" -213.3639 815.5 "?" -214.1189 134014 "b3/1.3ppm" -215.1223 10299.5 "b3+i/4.2ppm" -216.0974 817.8 "?" -217.0823 3500.5 "Int/SE/1.9ppm" -219.3852 836 "?" -222.1242 2551.5 "?" -225.0991 4462.1 "?" -226.1194 1819.1 "?" -229.1181 6277.7 "Int/EV/-0.8ppm,Int/VE/-0.8ppm" -234.0992 1302.3 "?" -240.1345 21406.7 "?" -240.2198 882.5 "?" -241.1192 1989.1 "y2-H2O-NH3/3.8ppm" -241.1384 1684 "?" -242.1143 4233 "?" -242.1492 2778.4 "?" -245.159 792.8 "?" -246.0991 2154.2 "?" -248.0698 1487.8 "?" -249.5848 765.4 "?" -254.1259 3540.4 "?" -256.1303 1530 "?" -256.1659 7535.6 "?" -257.1612 23103.1 "a4/1.5ppm" -258.1451 53196.9 "y2-H2O/1.0ppm" -258.1656 1886.8 "a4+i/7.9ppm" -259.1288 853.6 "y2-NH3/-0.2ppm" -259.1489 5333.4 "y2-H2O+i/4.5ppm" -264.1097 4168.1 "?" -271.1408 4874.5 "?" -276.1557 43313.6 "y2/1.1ppm" -277.1596 3627.4 "y2+i/4.7ppm" -282.1198 11960 "?" -282.1816 6243.1 "?" -285.156 70721.5 "b4/0.9ppm" -286.1596 8357.3 "b4+i/3.8ppm" -287.0818 1676.5 "?" -297.1559 2764.6 "?" -299.2081 5654.7 "?" -301.1155 1445.2 "?" -304.1141 3271.6 "?" -313.1878 2255.8 "?" -317.2701 1126.7 "?" -327.1668 2255.7 "?" -327.2031 12335.3 "?" -328.2078 1419.9 "?" -335.1022 1102.7 "?" -339.1418 3562 "?" -339.2035 4082.1 "?" -342.1779 5278.6 "?" -349.2 1115 "?" -353.2187 6849.9 "?" -355.1979 2456.3 "?" -356.2301 1374.8 "?" -358.1734 2130.2 "?" -367.2096 3137.8 "?" -369.1535 1179.9 "?" -370.2455 9499.6 "a5/1.7ppm" -371.7008 1451.4 "?" -375.2245 22737.7 "y3/1.8ppm" -376.2279 2902.4 "y3+i/3.1ppm" -377.1941 3243 "?" -382.2082 1160.7 "?" -384.2241 4525.1 "?" -387.2456 808.8 "?" -395.2044 3097.1 "?" -398.1798 1390.3 "?" -398.2402 8369.5 "b5/1.0ppm" -399.2453 1433.5 "b5+i/6.6ppm" -400.2175 1477.6 "?" -403.1794 1108.1 "?" -410.2393 1431 "?" -411.1993 2611.8 "?" -426.174 4174.1 "?" -426.2353 1747 "?" -427.2651 2092.7 "a6/-2.9ppm" -429.2092 2139.1 "?" -438.2451 2016.2 "?" -442.1512 2548.8 "?" -445.1946 994.4 "?" -446.1353 1722.5 "?" -446.1718 782.1 "?" -448.2306 1471 "?" -452.2242 2380 "?" -453.2463 1807.1 "?" -455.2633 3775.5 "b6/4.5ppm" -456.2614 1187.7 "b6+i/-5.9ppm" -464.1446 2120.7 "?" -466.2422 2050.7 "?" -471.2578 1806.9 "?" -481.1747 1118.1 "?" -481.7297 1115.4 "?" -486.2584 3180.9 "y4-H2O/5.3ppm" -490.2189 926.9 "?" -493.6116 940.7 "?" -497.2721 1445.6 "?" -499.1761 1383.7 "?" -499.2096 1262.8 "?" -504.2672 7049.8 "y4/1.6ppm" -509.2856 1991.4 "?" -511.1755 1490.7 "?" -514.2988 1812.8 "a7/0.8ppm" -523.2655 1711.6 "?" -524.2858 2612.6 "b7-H2O/5.9ppm" -528.2141 1322.9 "?" -529.1837 4266.8 "?" -533.1689 1872.9 "?" -537.2779 2429.9 "?" -539.2598 3644.5 "?" -542.2928 3010.1 "b7/-0.9ppm" -545.1652 1079 "?" -551.2365 2625.4 "y10-H2O^2/2.5ppm" -558.207 1645.1 "?" -560.241 16379.1 "y10^2/1.1ppm" -560.7422 8232.7 "y10^2+i/0.8ppm" -561.2434 3759.2 "y10^2+2i/2.4ppm" -568.1938 3165.5 "?" -572.1788 1675.8 "?" -578.2861 791.5 "?" -580.2 1614.6 "?" -582.2279 1808.4 "?" -586.2057 5627.5 "?" -588.2178 1176.6 "?" -590.1881 4182.2 "?" -591.3 7035.6 "y5/2.7ppm" -592.2983 1474.8 "y5+i/-5.2ppm" -598.2061 3432.3 "?" -603.7555 4327.2 "y11^2/-1.5ppm" -604.2574 3681.9 "y11^2+i/-0.6ppm" -604.7579 1830.1 "y11^2+2i/-0.5ppm" -608.1992 3790.4 "?" -609.7359 1059.9 "?" -614.2427 879.6 "?" -616.2162 3935 "?" -623.2614 2442.2 "y12-H2O^2/-0.7ppm" -623.7656 1586.4 "y12-NH3^2/18.8ppm,y12-H2O^2+i/3.8ppm" -632.2682 9946.8 "y12^2/1.7ppm" -632.7701 6533.9 "y12^2+i/2.5ppm" -633.2712 1699.8 "y12^2+2i/3.5ppm" -633.3458 2821.6 "?" -634.7709 1205.1 "b14-H2O^2/1.7ppm" -644.2333 1023.6 "?" -644.3076 878.1 "?" -647.3327 849.1 "?" -651.3581 8999.6 "a8/1.3ppm" -652.3618 3348.4 "a8+i/2.7ppm" -655.2262 2820.6 "?" -660.3223 1516.4 "y6-H2O/3.6ppm" -661.3433 7606.5 "b8-H2O/2.5ppm" -662.3483 1380 "b8-H2O+i/5.9ppm" -667.2252 1019.2 "?" -671.2955 1260 "y13-H2O-NH3^2/7.3ppm" -673.2364 4309.7 "?" -674.2409 1688.8 "?" -678.331 8546.4 "y6/0.8ppm" -679.2707 1080.4 "?" -679.3559 8766.1 "b8/5.4ppm" -679.8054 1687.8 "y13-H2O^2/2.2ppm" -680.3547 2791.2 "b8+i/-0.4ppm" -681.2847 1116.1 "?" -681.3271 1145.8 "?" -685.2344 1975.1 "?" -688.8099 8557.9 "y13^2/1.1ppm" -689.3101 7798.1 "y13^2+i/-0.7ppm" -689.8142 1742.5 "y13^2+2i/4.4ppm" -691.1587 1303.4 "?" -699.2916 2484.3 "?" -707.2698 3527.4 "?" -708.3794 1450.8 "a9/0.9ppm" -715.3156 1258.6 "y14-H2O^2/-9.6ppm" -717.2615 3144.1 "?" -723.9021 865.2 "?" -724.2491 3238.7 "?" -724.3282 4615.4 "y14^2/0.7ppm" -724.8292 4285.8 "y14^2+i/0.1ppm" -725.333 1740.7 "y14^2+2i/4.4ppm" -727.2462 3281.9 "?" -728.2467 1480.9 "?" -736.3738 7438.2 "b9/0.2ppm" -737.3769 2791.2 "b9+i/0.7ppm" -742.2589 5818.1 "?" -742.3272 968.1 "?" diff --git a/implementations/python/examples/chinese_hamster_hcd_selected_head.mzlb.txt b/implementations/python/examples/chinese_hamster_hcd_selected_head.mzlb.txt deleted file mode 100644 index 4991bc3..0000000 --- a/implementations/python/examples/chinese_hamster_hcd_selected_head.mzlb.txt +++ /dev/null @@ -1,1279 +0,0 @@ - -MS:1003188|library name=examples/chinese_hamster_hcd_selected_head - - - - -MS:1003061|library spectrum name=AAAACALTPGPLADLAAR/2_1(4,C,CAM)_46eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=855.4538 -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[1]MS:1000045|collision energy=46 -[1]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=5538 -MS:1003203|constituent spectrum file="CHO-K1_bRPLC_C1.RAW.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=2 -MS:1000002|sample name="jhu_cho_brplc_cam" -MS:1000028|detector resolution=7500 -[2]MS:1000828|isolation window lower offset=0.95 -[2]UO:0000000|unit=MS:1000040|m/z -[3]MS:1000829|isolation window upper offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=8799173.32 -MS:1003086|precursor apex intensity=25273307.5 -MS:1000512|filter string="FTMS + p NSI d Full ms2 855.96@hcd35.00 [140.00-1725.00]" -MS:1003059|number of peaks=87 -[4]MS:1003275|other attribute name=Se -[4]MS:1003276|other attribute value=1(^G1:sc=8.13346e-015) - -MS:1000224|molecular mass=1710.9076 -MS:1000888|stripped peptide sequence=AAAACALTPGPLADLAAR -MS:1000041|charge state=2 -[1]MS:1001975|delta m/z=1.4 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1003208|experimental precursor monoisotopic m/z=855.455 -MS:1003169|proforma peptidoform sequence=AAAAC[Carbamidomethyl]ALTPGPLADLAAR -MS:1001117|theoretical mass=1708.89303961159 -[2]MS:1003048|number of enzymatic termini=2 -[2]MS:1001045|cleavage agent name=MS:1001251|Trypsin -[2]MS:1001112|n-terminal flanking residue=R -[2]MS:1001113|c-terminal flanking residue=L -[2]MS:1000885|protein accession="tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1" - -MS:1003079|total unassigned intensity fraction=0.2848 -MS:1003080|top 20 peak unassigned intensity fraction=0.1879 -MS:1003289|intensity of highest unassigned peak=0.45 -MS:1003290|number of unassigned peaks among top 20 peaks=4 - -143.0823 14791.5 b2/5.6ppm -153.2575 5008.6 ? -159.0917 11531.8 ? -162.5977 5804.6 ? -169.0972 12931.0 ? -175.1193 18211.1 y1/2.0ppm,IR/2.0ppm -194.0699 6011.0 ? -199.1074 6737.4 ? -201.7527 5576.3 ? -212.1051 13786.1 ? -214.1195 82269.8 b3/4.1ppm -229.1552 7852.0 ? -232.0764 28555.9 ? -249.1071 4670.7 ? -257.1633 15001.9 a4/9.7ppm -276.4497 5288.0 ? -283.1411 24965.9 ? -283.3943 5090.5 ? -285.1567 48285.5 b4/3.4ppm -302.1834 10558.9 ? -303.114 52736.6 ? -317.1891 6585.3 y3/-12.9ppm -345.1593 18050.6 ? -354.1793 31400.1 b5-NH2-CO-CH2SH/5.9ppm -356.1916 7124.1 ? -370.3776 6139.7 ? -371.6662 11983.3 ? -374.1505 34930.7 ? -416.2029 8953.6 ? -417.1931 16940.5 a5/3.9ppm -425.2171 15449.8 b6-NH2-CO-CH2SH/6.6ppm -428.2024 8874.5 m5:8-H2O/14.4ppm -428.249 6831.1 ? -430.278 30118.6 y4/1.8ppm -445.1886 57883.2 b5/5.0ppm -446.2049 8868.2 m5:8/-4.2ppm -457.1753 5403.5 ? -467.2682 6117.4 ? -469.2735 6906.4 ? -471.2018 9435.3 ? -487.2299 15480.3 ? -488.2367 13813.7 a6/16.6ppm -490.7795 12739.9 y10^2/-0.6ppm -491.2839 6651.0 y10+i^2/5.4ppm -495.9153 6370.5 ? -499.2364 5273.9 m4:8-H2O/6.2ppm -516.2236 49862.4 b6/0.2ppm -528.2323 9881.3 ? -530.2752 10333.1 ? -541.3164 7041.3 ? -545.308 6833.8 y5/7.0ppm -558.2726 23958.7 ? -570.3232 6006.3 ? -601.3148 11919.6 a7/3.6ppm -617.2834 5841.2 ? -617.3372 4342.1 ? -629.3052 22419.3 b7/-3.7ppm -641.3058 11147.2 m2:8-H2O/-2.7ppm -659.3259 9164.2 m2:8/11.8ppm -685.3383 6861.0 ? -712.3472 13798.2 b8-H2O/3.6ppm -730.3578 16426.3 b8/3.5ppm -826.4765 18892.5 y8/-2.0ppm -855.017 7062.7 ? -855.5167 249849.0 ? -856.523 57946.3 ? -883.4993 29383.7 y9/-0.3ppm -922.4447 6413.2 ? -934.4906 6605.4 ? -963.5431 13545.1 y10-NH3/17.9ppm -980.556 559065.0 y10/3.7ppm -981.5587 216762.0 y10+i/3.6ppm -1037.5859 14218.2 ? -1038.5812 9574.2 ? -1067.8983 6611.6 ? -1081.6041 179858.0 y11/3.8ppm -1082.6077 79540.9 y11+i/4.5ppm -1143.0283 6099.8 ? -1194.6899 106907.0 y12/4.9ppm -1195.6869 50339.1 y12+i/-0.1ppm -1265.7273 83029.7 y13/4.8ppm -1266.7281 42164.7 y13+i/3.2ppm -1390.1328 5531.5 ? -1395.6904 8549.2 ? -1425.7538 51400.1 y14/1.4ppm -1426.7601 40643.8 y14+i/3.8ppm -1496.7792 11918.3 y15/-6.5ppm - - -MS:1003061|library spectrum name=AAAACALTPGPLADLAAR/2_1(4,C,CAM)_53eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=855.4538 -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[1]MS:1000045|collision energy=53 -[1]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=6275 -MS:1003203|constituent spectrum file="RO-QC-141112_Betenbaugh_HK_Fraction46.raw.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=14 -MS:1000002|sample name="betenbaugh_hk2" -MS:1000028|detector resolution=15000 -[2]MS:1000828|isolation window lower offset=0.95 -[2]UO:0000000|unit=MS:1000040|m/z -[3]MS:1000829|isolation window upper offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=1776618.56 -MS:1003086|precursor apex intensity=12167259.65 -MS:1000512|filter string="FTMS + p NSI d Full ms2 855.95@hcd35.00 [140.00-1725.00]" -MS:1003059|number of peaks=204 -[4]MS:1003275|other attribute name=Se -[4]MS:1003276|other attribute value=1(^G1:sc=1.31932e-020) - -MS:1000224|molecular mass=1710.9076 -MS:1000888|stripped peptide sequence=AAAACALTPGPLADLAAR -MS:1000041|charge state=2 -[1]MS:1001975|delta m/z=4.2 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1003208|experimental precursor monoisotopic m/z=855.4574 -MS:1003169|proforma peptidoform sequence=AAAAC[Carbamidomethyl]ALTPGPLADLAAR -MS:1001117|theoretical mass=1708.89303961159 -[2]MS:1003048|number of enzymatic termini=2 -[2]MS:1001045|cleavage agent name=MS:1001251|Trypsin -[2]MS:1001112|n-terminal flanking residue=R -[2]MS:1001113|c-terminal flanking residue=L -[2]MS:1000885|protein accession="tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1" - -MS:1003079|total unassigned intensity fraction=0.3165 -MS:1003080|top 20 peak unassigned intensity fraction=0.142 -MS:1003289|intensity of highest unassigned peak=0.16 -MS:1003290|number of unassigned peaks among top 20 peaks=5 - -143.0814 9555.6 b2/-0.7ppm -169.097 5174.5 ? -171.1126 2428.2 ? -175.1069 1175.7 ? -175.1187 7806.9 y1/-1.4ppm,IR/-1.4ppm -178.0645 645.1 ? -181.0971 2623.7 ? -183.1495 1770.8 m11:12-CO/1.7ppm -185.0921 4004.0 ? -185.1288 983.4 m12:13/1.9ppm -199.1073 2854.3 ? -203.1022 2225.3 ? -203.412 489.7 ? -204.0803 4532.0 ? -211.1438 1671.5 m11:12/-1.4ppm -212.103 6959.1 y2-2NH3/0.2ppm -214.1185 23984.8 b3/-0.5ppm -215.0481 1035.3 ? -215.1219 1943.5 b3+i/2.3ppm -215.1392 1652.7 m7:8/0.8ppm -216.0967 632.6 ? -229.1299 970.3 y2-NH3/1.7ppm -231.1446 601.8 ? -232.0748 11826.6 ? -235.1929 547.3 ? -240.1344 3195.6 ? -242.1137 1025.5 ? -246.1558 1514.8 y2/-1.1ppm -255.1454 790.9 ? -256.1652 1376.9 ? -257.1605 3523.6 a4/-1.2ppm -258.0901 1119.1 ? -268.1656 1623.7 m6:8-H2O/0.1ppm -282.1807 1542.2 m11:13/-1.8ppm -283.14 10639.1 ? -284.1443 1021.0 ? -285.1555 11955.3 b4/-0.8ppm -286.1599 1072.8 b4+i/4.8ppm -286.1761 2533.2 m6:8/-0.1ppm -293.366 528.7 ? -298.177 1429.9 ? -302.1818 2634.5 ? -303.1121 15782.5 ? -304.1151 1344.9 ? -309.1558 945.0 ? -311.1712 2335.2 ? -317.1934 2115.0 y3/0.7ppm -327.2036 961.2 ? -328.1647 1131.6 ? -329.1273 3077.6 ? -331.1088 859.4 ? -337.2232 2252.0 m9:12-CO/-0.6ppm -339.2033 1220.8 ? -341.1834 794.7 ? -345.1589 6582.2 ? -346.1541 1361.2 ? -353.2189 1800.0 ? -354.1769 9317.5 b5-NH2-CO-CH2SH/-0.8ppm -355.1793 1293.7 b5-NH2-CO-CH2SH+i/-1.9ppm -356.1933 1800.3 ? -357.211 686.5 ? -358.2065 618.4 ? -363.3883 563.8 ? -365.2181 2776.2 y7^2/4.9ppm -366.2212 705.5 ? -368.1942 682.0 ? -369.3904 685.6 ? -370.4914 4171.5 ? -372.1714 835.1 ? -374.149 10475.6 ? -375.153 1112.5 ? -380.1929 960.8 ? -384.1859 584.6 ? -386.2027 978.1 ? -396.2243 975.1 ? -397.2071 1560.8 m11:14/-2.7ppm -398.2401 1130.2 ? -400.1644 4875.2 ? -401.1676 730.6 ? -402.1434 1170.3 ? -408.2588 885.8 m9:13-CO/-4.2ppm -410.2415 678.5 ? -416.1944 2264.1 ? -417.192 3203.6 a5/1.3ppm -418.1938 714.5 a5+i/-0.6ppm -422.2396 762.6 ? -425.2144 2490.8 b6-NH2-CO-CH2SH/0.2ppm -428.1953 1647.7 m5:8-H2O/-2.1ppm -430.2767 20600.0 y4/-1.3ppm -431.2812 3236.0 y4+i/2.9ppm -436.2548 3128.6 m9:13/-1.5ppm -442.2117 1223.9 ? -445.1862 10843.9 b5/-0.4ppm -446.1865 1519.0 b5+i/-5.6ppm -446.2101 1269.8 m5:8/7.4ppm -454.23 854.8 ? -459.2378 1549.6 ? -471.2021 2150.3 ? -473.1871 733.9 ? -474.2351 776.1 ? -487.2318 3002.2 ? -488.2279 2861.1 a6/-1.4ppm -490.7802 1998.5 y10^2/0.8ppm -493.2748 802.6 ? -499.2884 798.8 ? -505.2755 1577.1 ? -513.2489 2142.4 ? -516.223 7108.2 b6/-1.0ppm -517.22 1175.7 b6+i/-11.9ppm -528.2206 1033.3 ? -528.2757 1044.1 y5-NH3/-3.7ppm -530.2791 1202.4 ? -533.272 1261.5 ? -535.1867 572.4 ? -543.2589 744.4 ? -545.3041 3290.4 y5/-0.2ppm -546.2418 626.0 ? -546.3103 815.6 y5+i/6.2ppm -551.2829 4018.4 m9:14/0.9ppm -552.287 815.2 m9:14+i/3.0ppm -558.2695 4055.3 ? -559.2736 821.5 ? -570.2687 978.2 m3:8-H2O/-3.1ppm -588.277 1266.6 m3:8/-6.8ppm -601.3116 1037.7 a7/-1.7ppm -609.3334 1558.5 ? -616.3435 2514.4 y6/3.6ppm -629.3079 1030.1 b7/0.5ppm -636.3726 1099.2 m9:15-CO/1.7ppm -638.3498 623.7 ? -641.3058 1372.7 m2:8-H2O/-2.7ppm -659.3138 896.8 m2:8/-6.6ppm -664.3644 2215.2 m9:15/-3.1ppm -665.3702 616.9 m9:15+i/1.2ppm -698.652 964.9 ? -710.8712 676.6 ? -712.343 766.7 b8-H2O/-2.3ppm -728.644 669.7 ? -729.4229 1339.5 y7/-3.4ppm -730.3568 859.0 b8/2.1ppm -735.4047 1839.2 m9:16/1.5ppm -735.7518 597.0 ? -736.4097 726.4 b9-NH2-CO-CH2SH/14.8ppm,m9:16+i/4.3ppm -758.5785 584.4 ? -804.5634 599.5 ? -806.4404 871.1 m9:17/-0.3ppm -807.4396 706.8 m9:17+i/-5.0ppm -809.4468 1047.0 y8-NH3/-5.9ppm -826.4767 5889.7 y8/-1.7ppm -827.4818 1704.1 y8+i/1.0ppm -835.4305 6503.5 ? -836.4305 855.7 ? -855.5272 1972.3 ? -883.499 11027.3 y9/-0.7ppm -884.5011 4136.3 y9+i/-1.5ppm -920.521 899.9 ? -922.4631 6661.9 ? -923.4683 1004.4 ? -938.5323 694.4 ? -954.0876 657.8 ? -962.5461 1056.8 y10-H2O/4.5ppm -963.5266 5559.2 y10-NH3/0.8ppm -964.5276 3037.9 y10-NH3+i/-1.1ppm -980.5516 101168.0 y10/-0.8ppm -981.5547 48825.1 y10+i/-0.5ppm -982.556 3169.3 y10+2i/-1.8ppm -998.153 653.4 ? -1026.4183 641.1 ? -1033.4918 1042.9 ? -1037.5729 7440.8 ? -1038.5754 4253.3 ? -1050.5208 5312.6 ? -1063.5883 1995.7 y11-H2O/-1.1ppm -1064.5804 1437.3 y11-NH3/6.5ppm,y11-H2O+i/-11.2ppm -1081.5985 28537.7 y11/-1.4ppm -1082.6017 16194.1 y11+i/-1.1ppm -1083.5983 1228.4 y11+2i/-6.6ppm -1150.6531 1305.7 ? -1176.6824 1518.9 y12-H2O/7.5ppm -1177.6671 1170.1 y12-NH3/8.1ppm,y12-H2O+i/-7.9ppm -1182.254 639.1 ? -1194.6826 20850.2 y12/-1.3ppm -1195.6853 12324.9 y12+i/-1.4ppm -1197.5858 4604.9 ? -1221.6934 1065.9 ? -1247.7007 1013.5 y13-H2O/-8.0ppm -1252.6328 702.9 ? -1265.7198 16380.4 y13/-1.1ppm -1266.7246 9779.2 y13+i/0.4ppm -1267.7239 747.9 y13+2i/-2.2ppm -1298.6331 3899.6 ? -1334.7629 576.6 y14-NH2-CO-CH2SH/15.2ppm -1395.6888 9418.6 ? -1396.6947 2451.5 ? -1407.7356 1083.1 y14-H2O/-4.0ppm -1408.7473 1011.7 y14-NH3/15.6ppm,y14-H2O+i/2.3ppm -1425.7515 7609.8 y14/-0.3ppm -1426.7562 7554.0 y14+i/1.1ppm -1466.0739 798.5 ? -1495.1215 635.8 ? -1496.7932 1534.6 y15/2.8ppm -1497.7944 1455.0 y15+i/1.7ppm -1557.3423 600.8 ? -1628.3004 719.6 ? - - -MS:1003061|library spectrum name=AAAAGQTGTVPPGAPGALPLPGMAIVK/2_0_76eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=1207.1672 -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[1]MS:1000045|collision energy=76 -[1]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=7528 -MS:1003203|constituent spectrum file="RO-QC-141112_Betenbaugh_HK_Fraction18.raw.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=2 -MS:1000002|sample name="betenbaugh_hk1" -MS:1000028|detector resolution=15000 -[2]MS:1000828|isolation window lower offset=0.95 -[2]UO:0000000|unit=MS:1000040|m/z -[3]MS:1000829|isolation window upper offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=6939079.2 -MS:1003086|precursor apex intensity=7583304.35 -MS:1000512|filter string="FTMS + p NSI d Full ms2 1207.67@hcd35.00 [140.00-2000.00]" -MS:1003059|number of peaks=122 -[4]MS:1003275|other attribute name=Se -[4]MS:1003276|other attribute value=1(^G1:sc=1.43642e-012) - -MS:1000224|molecular mass=2414.3344 -MS:1000888|stripped peptide sequence=AAAAGQTGTVPPGAPGALPLPGMAIVK -MS:1000041|charge state=2 -[1]MS:1001975|delta m/z=-0.9 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1003208|experimental precursor monoisotopic m/z=1207.1661 -MS:1003169|proforma peptidoform sequence=AAAAGQTGTVPPGAPGALPLPGMAIVK -MS:1001117|theoretical mass=2412.319901150229 -[2]MS:1003048|number of enzymatic termini=1 -[2]MS:1001045|cleavage agent name=MS:1001251|Trypsin -[2]MS:1001112|n-terminal flanking residue=A -[2]MS:1001113|c-terminal flanking residue=E -[2]MS:1000885|protein accession="tr|G3I2Q7|G3I2Q7_CRIGR Transcription intermediary factor 1-beta OS=Cricetulus griseus GN=I79_017700 PE=4 SV=1" - -MS:1003079|total unassigned intensity fraction=0.2591 -MS:1003080|top 20 peak unassigned intensity fraction=0.0 -MS:1003289|intensity of highest unassigned peak=0.12 -MS:1003290|number of unassigned peaks among top 20 peaks=0 - -143.0816 2935.3 b2/0.7ppm -147.1127 2210.5 y1/-0.7ppm -154.4137 1587.1 ? -155.0816 2825.2 m12:13/0.6ppm -169.771 1665.2 ? -176.5942 1535.3 ? -181.0984 2034.3 ? -186.0873 2509.4 ? -198.5815 1458.2 ? -199.2009 1692.3 ? -206.924 1799.6 ? -214.1185 6874.5 b3/-0.5ppm -214.6242 1695.0 ? -216.197 1659.5 ? -224.6321 1496.3 ? -226.1183 6292.8 m12:14/-1.4ppm -227.4689 1609.1 ? -230.1134 2157.9 ? -240.1377 1613.7 ? -246.1817 2500.8 y2/2.0ppm -252.1353 2976.9 m11:13/4.1ppm -257.1249 2901.5 ? -257.1618 2468.8 a4/3.8ppm -266.3697 1813.9 ? -283.6819 1747.3 ? -285.1557 5707.9 b4/-0.1ppm -285.8154 1730.9 ? -287.1343 2200.9 ? -295.139 1768.2 ? -295.1769 3116.9 m12:15-CO/1.5ppm,m11:14-CO/1.5ppm -323.1715 9768.4 m12:15/0.4ppm,m11:14/0.4ppm -326.1471 1541.0 ? -328.1606 3372.4 ? -339.2022 4142.5 m15:18/-1.4ppm -342.1785 2123.8 b5/3.8ppm -357.1593 8559.3 m21:24/0.6ppm -368.2019 1424.3 ? -370.1709 2286.1 ? -382.171 2478.3 ? -399.199 2560.8 ? -404.719 1744.2 ? -411.2023 1764.9 ? -412.2186 2214.1 ? -416.1802 1569.1 ? -425.2139 2586.2 ? -427.1956 2391.1 ? -436.2577 3485.4 m15:19/5.2ppm -442.2464 3103.3 a6/12.5ppm -470.2405 9151.0 b6/10.1ppm -496.2594 3078.1 m19:23/1.2ppm -498.2301 3109.0 ? -520.2899 2739.1 m11:17-CO/4.0ppm -526.2617 3852.0 ? -539.2985 1828.0 m19:24-CO/-4.7ppm -548.2831 5503.1 m11:17/0.7ppm -549.339 5105.4 m15:20/-0.9ppm -557.2015 1790.3 ? -564.3132 2803.2 m12:18/-1.5ppm -564.4461 1473.4 ? -567.2952 5860.9 m19:24/-1.3ppm -569.3114 4720.3 m21:26/-0.3ppm -571.2812 2601.4 b7/-3.9ppm -592.1807 1899.1 ? -614.3491 1751.3 ? -633.3705 7963.1 m12:19-CO/-2.2ppm,m11:18-CO/-2.2ppm -640.3058 2814.4 ? -661.3663 17369.3 m12:19/-0.7ppm,m11:18/-0.7ppm -662.3647 3974.4 m12:19+i/-7.5ppm,m11:18+i/-7.5ppm -680.3803 6159.2 m19:25/0.5ppm -687.8984 2815.3 y15-NH3^2/5.9ppm -695.8273 4004.9 ? -699.8309 1878.5 ? -706.7814 1733.4 ? -711.3409 9244.0 b9-H2O/-1.6ppm -715.4171 25528.5 y7/0.0ppm -716.4193 6624.9 y7+i/-0.9ppm -720.4687 1548.7 ? -740.657 1772.0 ? -747.7864 1728.5 ? -774.4467 2604.0 m12:20/-5.4ppm -779.444 3102.9 m19:26/-5.7ppm -792.3951 2288.2 ? -792.5062 1866.9 ? -793.287 2259.9 ? -793.4606 4623.5 y17^2/0.3ppm -793.9547 2201.9 y17+i^2/-9.0ppm -843.5064 6631.8 m12:21-CO/-2.7ppm,m11:20-CO/-2.7ppm -871.5032 16269.2 m12:21/-0.5ppm,m11:20/-0.5ppm -872.5042 2808.0 m12:21+i/-2.7ppm,m11:20+i/-2.7ppm -905.4965 3245.9 m15:24/5.7ppm -925.5524 22654.0 y9/-1.7ppm -926.5582 6169.9 y9+i/1.5ppm -1025.5756 3014.9 m11:22/-2.2ppm -1038.6364 3465.3 y10/-1.5ppm -1050.3751 1648.4 ? -1101.6609 1971.4 ? -1156.626 2932.8 m11:23/6.6ppm -1227.1982 1647.0 ? -1227.6581 3903.5 m11:24/2.2ppm -1263.7479 15942.2 y13/-1.1ppm -1264.757 6224.1 y13+i/3.8ppm -1334.7977 1960.4 y14/8.4ppm -1340.7531 3560.4 m11:25/10.1ppm -1356.4097 1828.1 ? -1391.7969 3956.8 y15/-7.9ppm -1392.7919 2490.2 y15+i/-13.6ppm -1402.2483 2181.2 ? -1466.1517 2524.0 ? -1482.8165 2498.3 ? -1488.8579 7946.7 y16/-1.9ppm -1489.8688 4824.6 y16+i/3.5ppm -1510.2008 2208.8 ? -1511.4255 4721.0 ? -1522.1158 2439.5 ? -1554.3594 1714.9 ? -1567.8997 3204.8 y17-H2O/-2.0ppm -1585.9117 37792.9 y17/-1.1ppm -1586.9141 23000.3 y17+i/-1.4ppm -1612.5677 1607.6 ? -1616.5776 4065.9 ? -1752.5294 2175.8 ? -1980.9857 3567.9 ? - - -MS:1003061|library spectrum name=AAAAGSTSVKPIFSR/2_0_44eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=731.9043 -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[1]MS:1000045|collision energy=44 -[1]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=3052 -MS:1003203|constituent spectrum file="RO-QC-141112_Betenbaugh_HK_Fraction26.raw.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=4 -MS:1000002|sample name="betenbaugh_hk4" -MS:1000028|detector resolution=15000 -[2]MS:1000828|isolation window lower offset=0.95 -[2]UO:0000000|unit=MS:1000040|m/z -[3]MS:1000829|isolation window upper offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=324419.29 -MS:1003086|precursor apex intensity=361702.23 -MS:1000512|filter string="FTMS + p NSI d Full ms2 731.90@hcd34.00 [110.00-1475.00]" -MS:1003059|number of peaks=111 -[4]MS:1003275|other attribute name=Se -[4]MS:1003276|other attribute value=1(^G1:sc=6.33525e-018) - -MS:1000224|molecular mass=1463.8086 -MS:1000888|stripped peptide sequence=AAAAGSTSVKPIFSR -MS:1000041|charge state=2 -[1]MS:1001975|delta m/z=-2.7 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1003208|experimental precursor monoisotopic m/z=731.9023 -MS:1003169|proforma peptidoform sequence=AAAAGSTSVKPIFSR -MS:1001117|theoretical mass=1461.7939769138902 -[2]MS:1003048|number of enzymatic termini=1 -[2]MS:1001045|cleavage agent name=MS:1001251|Trypsin -[2]MS:1001112|n-terminal flanking residue=Q -[2]MS:1001113|c-terminal flanking residue=D -[2]MS:1000885|protein accession="tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1" - -MS:1003079|total unassigned intensity fraction=0.1681 -MS:1003080|top 20 peak unassigned intensity fraction=0.0217 -MS:1003289|intensity of highest unassigned peak=0.17 -MS:1003290|number of unassigned peaks among top 20 peaks=1 - -110.1269 76.26 ? -113.4028 68.16 ? -115.0865 659.49 a2/-0.8ppm -129.1022 463.28 IK/-0.3ppm -129.9147 62.91 ? -129.9924 68.35 ? -143.0815 2091.84 b2/0.0ppm -145.1529 69.39 ? -167.7261 67.46 ? -169.0972 508.54 ? -175.1189 354.1 y1/-0.3ppm,IK/-0.3ppm,IR/-0.3ppm -183.1488 80.6 m11:12-CO/-2.1ppm -200.1034 223.41 ? -214.1187 2461.15 b3/0.4ppm -215.1224 150.92 b3+i/4.6ppm -226.1194 166.15 ? -228.0984 104.95 ? -228.1709 81.16 m9:10/1.1ppm -231.5444 76.88 ? -240.136 109.39 ? -242.1143 129.58 ? -256.1299 117.54 ? -257.1609 174.31 a4/0.3ppm -262.1501 113.33 y2/-3.4ppm -264.371 72.61 ? -269.1243 138.11 ? -270.1455 122.57 ? -271.1404 453.74 ? -281.1254 95.19 ? -283.6823 109.92 ? -285.1563 279.13 b4/2.0ppm -287.135 187.61 ? -287.8068 65.78 ? -297.1195 79.71 ? -297.1555 129.0 ? -299.1343 183.34 ? -314.1814 114.14 a5/-2.8ppm -314.954 72.12 ? -315.1298 108.82 ? -342.1795 136.49 b5/6.7ppm -357.3935 72.21 ? -358.2114 117.32 m11:13/-3.1ppm -370.173 101.69 ? -374.2291 100.25 y6^2/-0.3ppm -384.186 84.78 ? -390.441 73.17 ? -392.1888 108.06 y3-NH3/-10.3ppm -409.2202 184.35 y3/2.0ppm -411.2 90.17 b6-H2O/3.3ppm -413.199 69.51 ? -432.1567 69.03 ? -457.2071 70.57 ? -467.2223 88.32 ? -467.28 113.01 y8^2/1.2ppm -469.7274 63.86 ? -517.8033 126.12 y9^2/0.0ppm -522.3049 76.1 y4/2.8ppm -523.8322 67.7 ? -551.1071 72.33 ? -556.2686 106.48 ? -561.3188 193.75 y10^2/-0.9ppm -561.8202 108.62 y10+i^2/-1.0ppm -589.8297 605.37 y11^2/-0.6ppm -590.3306 217.12 y11+i^2/-1.5ppm -602.33 179.57 y5-NH3/0.5ppm -613.2793 68.37 ? -619.356 2943.26 y5/-0.4ppm -620.3603 685.92 y5+i/1.9ppm -625.349 501.99 y12^2/0.7ppm -625.8499 293.9 y12+i^2/-0.2ppm -626.1416 61.18 ? -660.8675 419.89 y13^2/0.5ppm -661.3681 249.76 y13+i^2/-0.7ppm -667.6551 76.13 ? -690.5546 80.2 ? -691.2347 99.99 ? -696.3888 148.08 y14^2/4.4ppm -696.8864 94.95 y14+i^2/-1.1ppm -699.1979 125.04 ? -703.2349 88.5 ? -707.3016 78.55 ? -723.7889 71.89 ? -730.4289 91.25 y6-NH3/5.8ppm -731.903 327.43 p/-1.7ppm -732.4063 260.03 p+i/0.8ppm -747.4508 1511.3 y6/-0.5ppm -748.4523 477.25 y6+i/-2.3ppm -813.9755 73.74 ? -814.2291 68.08 ? -846.5192 787.5 y7/-0.5ppm -847.5187 219.01 y7+i/-4.5ppm -933.5519 1204.76 y8/0.3ppm -934.5554 585.8 y8+i/1.0ppm -1034.5983 1246.92 y9/-1.0ppm -1035.6029 562.43 y9+i/0.7ppm -1043.6613 80.22 ? -1078.0837 77.1 ? -1121.6309 955.3 y10/-0.4ppm -1122.6306 445.79 y10+i/-3.2ppm -1160.6473 138.54 y11-H2O/4.4ppm -1161.6349 262.21 y11-NH3/7.4ppm,y11-H2O+i/-8.8ppm -1178.6521 2592.9 y11/-0.6ppm -1179.6555 1376.21 y11+i/-0.1ppm -1182.3555 67.85 ? -1198.9932 63.25 ? -1249.6902 1081.82 y12/0.2ppm -1250.691 611.72 y12+i/-1.4ppm -1320.7277 504.87 y13/0.5ppm -1321.7318 253.18 y13+i/1.5ppm -1389.0188 62.97 ? -1465.9423 113.63 ? - - -MS:1003061|library spectrum name=AAAAGSTSVKPIFSR/3_0_28eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=488.2719 -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[1]MS:1000045|collision energy=28 -[1]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=2890 -MS:1003203|constituent spectrum file="RO-QC-141112_Betenbaugh_HK_Fraction26.raw.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=5 -MS:1000002|sample name="betenbaugh_hk3" -MS:1000028|detector resolution=15000 -[2]MS:1000828|isolation window lower offset=0.95 -[2]UO:0000000|unit=MS:1000040|m/z -[3]MS:1000829|isolation window upper offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=3390555.93 -MS:1003086|precursor apex intensity=3965011.86 -MS:1000512|filter string="FTMS + p NSI d Full ms2 488.27@hcd34.00 [110.00-1475.00]" -MS:1003059|number of peaks=161 -[4]MS:1003275|other attribute name=Se -[4]MS:1003276|other attribute value=1(^G1:sc=9.67069e-018) - -MS:1000224|molecular mass=1464.8157 -MS:1000888|stripped peptide sequence=AAAAGSTSVKPIFSR -MS:1000041|charge state=3 -[1]MS:1001975|delta m/z=3.8 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1003208|experimental precursor monoisotopic m/z=488.2738 -MS:1003169|proforma peptidoform sequence=AAAAGSTSVKPIFSR -MS:1001117|theoretical mass=1461.7939769138902 -[2]MS:1003048|number of enzymatic termini=1 -[2]MS:1001045|cleavage agent name=MS:1001251|Trypsin -[2]MS:1001112|n-terminal flanking residue=Q -[2]MS:1001113|c-terminal flanking residue=D -[2]MS:1000885|protein accession="tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1" - -MS:1003079|total unassigned intensity fraction=0.1804 -MS:1003080|top 20 peak unassigned intensity fraction=0.0 -MS:1003289|intensity of highest unassigned peak=0.09 -MS:1003290|number of unassigned peaks among top 20 peaks=0 - -110.4751 880.7 ? -111.5315 809.7 ? -112.087 1086.3 IR/0.7ppm -115.0865 75818.4 a2/-0.8ppm -116.0703 1405.8 IR/-2.6ppm -116.0899 1580.2 a2+i/5.4ppm -120.0808 2176.9 IF/0.2ppm -129.0659 3793.3 ? -129.1022 29530.7 IK/-0.3ppm -130.1056 1054.6 IK+i/4.4ppm -138.138 996.1 ? -143.0815 89938.4 b2/0.0ppm -144.0849 3848.2 b2+i/4.2ppm -144.8468 964.9 ? -145.0606 3718.8 ? -153.0659 1282.7 ? -158.0922 2201.6 y1-NH3/-1.3ppm -159.1125 2211.3 ? -160.572 774.2 ? -161.0918 1971.8 ? -163.5364 927.8 ? -169.0971 8412.0 ? -171.0764 6416.5 ? -175.1189 8291.0 y1/-0.3ppm,IK/-0.3ppm,IR/-0.3ppm -177.5624 849.9 ? -183.1492 2806.4 m11:12-CO/0.1ppm -185.0934 958.0 ? -189.0877 3809.0 ? -198.0881 3160.3 ? -200.103 8672.6 ? -204.5067 880.9 ? -210.0874 2471.9 ? -211.1447 2133.4 m11:12/2.8ppm -214.1187 22627.3 b3/0.4ppm -215.1205 976.2 b3+i/-4.2ppm -216.0981 4203.5 ? -228.0981 5566.6 y2-2NH3/1.0ppm -228.1706 4194.9 m9:10/-0.2ppm -240.0988 1395.3 ? -240.1342 1105.3 ? -242.1136 2814.5 ? -244.1677 932.4 ? -245.1246 2188.3 y2-NH3/0.7ppm -257.1618 1137.5 a4/3.8ppm -258.1086 4986.3 ? -262.1516 3577.0 y2/2.4ppm -269.1245 3938.1 ? -270.1448 3287.2 ? -271.1396 2172.6 ? -275.3359 1037.0 ? -276.1198 996.0 ? -276.2175 843.1 ? -281.1246 2464.1 ? -281.1612 873.4 ? -285.157 1116.3 b4/4.5ppm -287.136 3444.7 ? -297.1196 5420.4 ? -299.1352 5315.0 ? -310.1825 3745.4 y5^2/2.4ppm -315.1301 9824.1 ? -323.1358 1153.1 ? -333.1407 1547.3 ? -339.168 816.3 ? -352.1606 1609.5 ? -357.1775 2103.4 ? -365.7159 1399.2 y6-NH3^2/-0.2ppm -368.1564 3740.4 ? -370.1726 2557.4 ? -374.2292 5561.8 y6^2/-0.1ppm -374.7322 1301.0 y6+i^2/4.1ppm -376.1832 956.2 ? -378.174 956.5 ? -386.167 4098.3 ? -386.2034 1795.4 ? -392.193 3698.0 y3-NH3/0.4ppm -395.407 759.9 ? -396.188 2827.1 ? -404.1751 1611.3 ? -404.2145 1149.9 ? -409.2199 7096.2 y3/1.2ppm -414.1984 3857.6 ? -420.7338 881.9 ? -421.1867 1530.4 ? -424.0701 904.3 ? -439.1948 1910.9 ? -440.9135 938.0 y13^3/-0.8ppm -457.2043 2679.7 ? -467.2251 3238.5 ? -467.2799 6142.0 y8^2/1.0ppm -467.7818 2674.9 y8+i^2/1.9ppm -485.2344 2370.1 ? -508.7988 1318.3 y9-H2O^2/1.6ppm -517.804 8711.4 y9^2/1.4ppm -518.305 5346.7 y9+i^2/0.5ppm -520.2481 1151.1 ? -522.3037 4970.1 y4/0.5ppm -534.7964 1651.3 ? -538.2622 1220.7 ? -552.317 2102.2 y10-H2O^2/5.4ppm -556.27 960.1 ? -558.8151 1054.4 ? -561.3193 9865.4 y10^2/0.0ppm -561.8219 3932.3 y10+i^2/2.1ppm -580.8237 4086.9 y11-H2O^2/-1.8ppm -581.3318 1582.3 y11-H2O+i^2/9.7ppm -589.8302 30985.9 y11^2/0.3ppm -590.3312 15287.5 y11+i^2/-0.5ppm -601.3485 2836.0 y5-H2O/4.7ppm -602.3292 3454.7 y5-NH3/-0.8ppm -603.3347 1573.2 y5-NH3+i/3.5ppm -604.2908 937.8 ? -607.3416 3013.0 ? -616.3441 2761.9 y12-H2O^2/1.3ppm -616.8438 2753.7 y12-NH3^2/13.8ppm,y12-H2O+i^2/-1.5ppm -617.736 1000.9 ? -619.3562 112581.0 y5/0.0ppm -619.4061 1331.1 ? -620.3597 26856.2 y5+i/1.0ppm -625.3489 29725.9 y12^2/0.5ppm -625.8499 17686.6 y12+i^2/-0.2ppm -651.8593 1435.9 y13-H2O^2/-3.9ppm -660.8666 17322.8 y13^2/-0.8ppm -661.3691 10845.8 y13+i^2/0.8ppm -665.7083 857.4 ? -677.8406 865.0 ? -679.6729 1028.1 ? -692.6226 1839.8 ? -696.39 1380.5 y14^2/6.2ppm -696.8853 1825.9 y14+i^2/-2.6ppm -712.8559 1575.5 ? -729.4384 2131.4 y6-H2O/-3.0ppm -730.4251 3172.7 y6-NH3/0.6ppm -743.5792 878.1 ? -747.4517 51670.9 y6/0.7ppm -748.454 16389.8 y6+i/-0.1ppm -846.519 23172.3 y7/-0.7ppm -847.5219 8878.0 y7+i/-0.7ppm -888.9458 1103.0 ? -915.5491 1402.6 y8-H2O/8.8ppm -916.5312 1566.9 y8-NH3/6.7ppm,y8-H2O+i/-13.9ppm -933.5517 34961.3 y8/0.1ppm -934.5549 14638.2 y8+i/0.4ppm -962.5909 952.1 ? -967.9422 926.5 ? -1016.5936 1298.4 y9-H2O/4.8ppm -1017.5724 1109.4 y9-NH3/-0.3ppm,y9-H2O+i/-18.9ppm -1034.5992 17085.6 y9/-0.1ppm -1035.6008 7940.0 y9+i/-1.3ppm -1049.6464 924.5 ? -1068.5891 1068.8 ? -1072.3027 820.3 ? -1100.4142 824.6 ? -1121.6331 6228.7 y10/1.6ppm -1122.6238 3007.6 y10+i/-9.3ppm -1178.6527 11088.9 y11/-0.1ppm -1179.6552 6228.8 y11+i/-0.4ppm -1249.6901 2527.6 y12/0.2ppm -1250.6986 1715.0 y12+i/4.7ppm -1347.309 852.2 ? -1465.9084 1527.1 ? -1469.9915 925.5 ? - - -MS:1003061|library spectrum name=AAAALGSHGSCSSEVEK/2_1(10,C,CAM)_50eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=830.8834 -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[1]MS:1000045|collision energy=50 -[1]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=1185 -MS:1003203|constituent spectrum file="RO-QC-141112_Betenbaugh_HK_Fraction18.raw.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=2 -MS:1000002|sample name="betenbaugh_hk5" -MS:1000028|detector resolution=15000 -[2]MS:1000828|isolation window lower offset=0.95 -[2]UO:0000000|unit=MS:1000040|m/z -[3]MS:1000829|isolation window upper offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=30003.73 -MS:1003086|precursor apex intensity=28800.11 -MS:1000512|filter string="FTMS + p NSI d Full ms2 831.38@hcd34.00 [110.00-1675.00]" -MS:1003059|number of peaks=68 -[4]MS:1003275|other attribute name=Se -[4]MS:1003276|other attribute value=1(^G1:sc=6.94218e-013) - -MS:1000224|molecular mass=1661.7668 -MS:1000888|stripped peptide sequence=AAAALGSHGSCSSEVEK -MS:1000041|charge state=2 -[1]MS:1001975|delta m/z=4.1 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1003208|experimental precursor monoisotopic m/z=830.8868 -MS:1003169|proforma peptidoform sequence=AAAALGSHGSC[Carbamidomethyl]SSEVEK -MS:1001117|theoretical mass=1659.7522486039798 -[2]MS:1003048|number of enzymatic termini=2 -[2]MS:1001045|cleavage agent name=MS:1001251|Trypsin -[2]MS:1001112|n-terminal flanking residue=K -[2]MS:1001113|c-terminal flanking residue=E -[2]MS:1000885|protein accession="tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1" - -MS:1003079|total unassigned intensity fraction=0.4368 -MS:1003080|top 20 peak unassigned intensity fraction=0.184 -MS:1003289|intensity of highest unassigned peak=0.45 -MS:1003290|number of unassigned peaks among top 20 peaks=6 - -110.1102 57.808 ? -115.0864 84.449 a2/-1.6ppm -128.1915 60.078 ? -129.1023 157.87 IK/0.5ppm,y1-H2O/0.5ppm -130.0863 143.466 y1-NH3/0.4ppm -134.6533 64.924 ? -143.0814 409.786 b2/-0.7ppm -147.1131 319.305 y1/2.0ppm -151.4513 63.288 ? -153.7949 64.094 ? -159.3516 66.632 ? -165.1407 62.763 ? -185.7231 56.05 ? -192.253 56.668 ? -206.6181 58.523 ? -207.8363 67.364 ? -214.1188 604.289 b3/0.9ppm -240.1356 101.032 ? -242.2549 68.729 ? -252.7986 69.267 ? -257.1606 92.981 a4/-0.8ppm -258.144 282.108 y2-H2O/-3.2ppm -276.1561 234.148 y2/2.5ppm -282.3431 71.242 ? -285.1556 363.637 b4/-0.5ppm -312.7774 62.146 ? -343.4806 65.426 ? -355.0699 104.479 ? -370.4347 269.799 ? -375.2243 139.559 y3/1.3ppm -385.774 62.977 ? -388.1424 58.351 ? -431.0488 72.382 ? -529.347 83.459 ? -598.1849 62.213 ? -688.806 84.319 y13^2/-4.6ppm -692.6966 113.075 ? -694.6636 75.382 ? -700.6682 128.47 ? -725.4309 81.78 ? -817.4878 85.857 ? -819.1156 63.497 ? -903.9632 63.514 ? -982.4142 289.221 y9/-0.4ppm -983.42 122.064 b11/-16.6ppm,y9+i/2.6ppm -1036.3802 70.607 ? -1104.5166 70.543 ? -1119.4768 195.679 y10/2.9ppm -1120.4703 107.369 y10+i/-5.3ppm -1139.4911 84.154 b13-H2O/1.1ppm -1206.5106 83.121 y11/4.2ppm -1263.5344 229.989 y12/5.9ppm -1264.5262 152.204 y12+i/-2.8ppm -1268.5361 75.921 b14-H2O/2.9ppm -1286.5446 234.168 b14/1.3ppm -1287.5588 119.455 b14+i/10.2ppm -1376.6179 122.497 y13/5.0ppm -1376.9817 67.739 ? -1451.4869 67.46 ? -1465.7048 143.33 ? -1480.5077 95.07 ? -1522.3134 127.307 ? -1554.5259 83.112 ? -1595.7773 67.148 ? -1608.2555 61.797 ? -1623.9801 102.29 ? -1628.4393 118.77 ? -1670.2889 140.136 ? - - -MS:1003061|library spectrum name=AAAALGSHGSCSSEVEK/2_1(10,C,CAM)_52eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=830.8834 -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[1]MS:1000045|collision energy=52 -[1]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=868 -MS:1003203|constituent spectrum file="RO-QC-141112_Betenbaugh_HK_Fraction19.raw.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=3 -MS:1000002|sample name="betenbaugh_hk2" -MS:1000028|detector resolution=15000 -[2]MS:1000828|isolation window lower offset=0.95 -[2]UO:0000000|unit=MS:1000040|m/z -[3]MS:1000829|isolation window upper offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=9544513.13 -MS:1003086|precursor apex intensity=26056925.91 -MS:1000512|filter string="FTMS + p NSI d Full ms2 830.88@hcd35.00 [140.00-1675.00]" -MS:1003059|number of peaks=402 -[4]MS:1003275|other attribute name=Se -[4]MS:1003276|other attribute value=1(^G1:sc=6.88234e-022) - -MS:1000224|molecular mass=1661.7668 -MS:1000888|stripped peptide sequence=AAAALGSHGSCSSEVEK -MS:1000041|charge state=2 -[1]MS:1001975|delta m/z=-2.0 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1003208|experimental precursor monoisotopic m/z=830.8817 -MS:1003169|proforma peptidoform sequence=AAAALGSHGSC[Carbamidomethyl]SSEVEK -MS:1001117|theoretical mass=1659.7522486039798 -[2]MS:1003048|number of enzymatic termini=2 -[2]MS:1001045|cleavage agent name=MS:1001251|Trypsin -[2]MS:1001112|n-terminal flanking residue=K -[2]MS:1001113|c-terminal flanking residue=E -[2]MS:1000885|protein accession="tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1" - -MS:1003079|total unassigned intensity fraction=0.339 -MS:1003080|top 20 peak unassigned intensity fraction=0.0816 -MS:1003289|intensity of highest unassigned peak=0.17 -MS:1003290|number of unassigned peaks among top 20 peaks=3 - -141.1024 1824.4 ? -143.0816 54472.6 b2/0.7ppm -144.0851 2028.2 b2+i/5.6ppm -147.1129 40570.6 y1/0.7ppm -148.1159 2104.9 y1+i/1.9ppm -151.6119 866.7 ? -157.0613 1472.8 m12:13-H2O/3.4ppm -157.0974 1742.9 y1-H2O+CO/1.6ppm -157.1335 2797.4 ? -158.3324 771.5 ? -158.4784 915.0 ? -165.0449 784.1 ? -169.0973 19654.9 ? -170.1011 1507.2 ? -170.2729 987.0 ? -175.0683 1008.2 m12:13/-17.3ppm -182.0172 1038.4 ? -183.113 1337.8 ? -183.1501 1174.6 ? -185.1288 4333.2 ? -195.0881 4158.9 ? -196.1971 908.9 ? -196.9482 1078.6 ? -197.1034 2784.1 ? -199.0719 3248.0 ? -200.1024 1115.3 ? -201.1237 7050.8 ? -209.4671 931.3 ? -211.1448 5058.2 ? -213.1236 1676.9 ? -213.3639 815.5 ? -214.1189 134014.0 b3/1.3ppm -215.1223 10299.5 b3+i/4.2ppm -216.0974 817.8 ? -217.0823 3500.5 m13:14/1.9ppm -219.3852 836.0 ? -222.1242 2551.5 ? -225.0991 4462.1 ? -226.1194 1819.1 ? -229.1181 6277.7 m14:15/-0.8ppm,m15:16/-0.8ppm -234.0992 1302.3 ? -240.1345 21406.7 ? -240.2198 882.5 ? -241.1192 1989.1 y2-H2O-NH3/3.8ppm -241.1384 1684.0 ? -242.1143 4233.0 ? -242.1492 2778.4 ? -245.159 792.8 ? -246.0991 2154.2 ? -248.0698 1487.8 ? -249.5848 765.4 ? -254.1259 3540.4 ? -256.1303 1530.0 ? -256.1659 7535.6 ? -257.1612 23103.1 a4/1.5ppm -258.1451 53196.9 y2-H2O/1.0ppm -258.1656 1886.8 a4+i/7.9ppm -259.1288 853.6 y2-NH3/-0.2ppm -259.1489 5333.4 y2-H2O+i/4.5ppm -264.1097 4168.1 ? -271.1408 4874.5 ? -276.1557 43313.6 y2/1.1ppm -277.1596 3627.4 y2+i/4.7ppm -282.1198 11960.0 ? -282.1816 6243.1 ? -285.156 70721.5 b4/0.9ppm -286.1596 8357.3 b4+i/3.8ppm -287.0818 1676.5 ? -297.1559 2764.6 ? -299.2081 5654.7 ? -301.1155 1445.2 ? -304.1141 3271.6 ? -313.1878 2255.8 ? -317.2701 1126.7 ? -327.1668 2255.7 ? -327.2031 12335.3 ? -328.2078 1419.9 ? -335.1022 1102.7 ? -339.1418 3562.0 ? -339.2035 4082.1 ? -342.1779 5278.6 ? -349.2 1115.0 ? -353.2187 6849.9 ? -355.1979 2456.3 ? -356.2301 1374.8 ? -358.1734 2130.2 ? -367.2096 3137.8 ? -369.1535 1179.9 ? -370.2455 9499.6 a5/1.7ppm -371.7008 1451.4 ? -375.2245 22737.7 y3/1.8ppm -376.2279 2902.4 y3+i/3.1ppm -377.1941 3243.0 ? -382.2082 1160.7 ? -384.2241 4525.1 ? -387.2456 808.8 ? -395.2044 3097.1 ? -398.1798 1390.3 ? -398.2402 8369.5 b5/1.0ppm -399.2453 1433.5 b5+i/6.6ppm -400.2175 1477.6 ? -403.1794 1108.1 ? -410.2393 1431.0 ? -411.1993 2611.8 ? -426.174 4174.1 ? -426.2353 1747.0 ? -427.2651 2092.7 a6/-2.9ppm -429.2092 2139.1 ? -438.2451 2016.2 ? -442.1512 2548.8 ? -445.1946 994.4 ? -446.1353 1722.5 ? -446.1718 782.1 ? -448.2306 1471.0 ? -452.2242 2380.0 ? -453.2463 1807.1 ? -455.2633 3775.5 b6/4.5ppm -456.2614 1187.7 b6+i/-5.9ppm -464.1446 2120.7 ? -466.2422 2050.7 ? -471.2578 1806.9 ? -481.1747 1118.1 ? -481.7297 1115.4 ? -486.2584 3180.9 y4-H2O/5.3ppm -490.2189 926.9 ? -493.6116 940.7 ? -497.2721 1445.6 ? -499.1761 1383.7 ? -499.2096 1262.8 ? -504.2672 7049.8 y4/1.6ppm -509.2856 1991.4 ? -511.1755 1490.7 ? -514.2988 1812.8 a7/0.8ppm -523.2655 1711.6 ? -524.2858 2612.6 b7-H2O/5.9ppm -528.2141 1322.9 ? -529.1837 4266.8 ? -533.1689 1872.9 ? -537.2779 2429.9 ? -539.2598 3644.5 ? -542.2928 3010.1 b7/-0.9ppm -545.1652 1079.0 ? -551.2365 2625.4 y10-H2O^2/2.5ppm -558.207 1645.1 ? -560.241 16379.1 y10^2/1.1ppm -560.7422 8232.7 y10+i^2/0.8ppm -561.2434 3759.2 y10+2i^2/2.4ppm -568.1938 3165.5 ? -572.1788 1675.8 ? -578.2861 791.5 ? -580.2 1614.6 ? -582.2279 1808.4 ? -586.2057 5627.5 ? -588.2178 1176.6 ? -590.1881 4182.2 ? -591.3 7035.6 y5/2.7ppm -592.2983 1474.8 y5+i/-5.2ppm -598.2061 3432.3 ? -603.7555 4327.2 y11^2/-1.5ppm -604.2574 3681.9 y11+i^2/-0.6ppm -604.7579 1830.1 y11+2i^2/-0.5ppm -608.1992 3790.4 ? -609.7359 1059.9 ? -614.2427 879.6 ? -616.2162 3935.0 ? -623.2614 2442.2 y12-H2O^2/-0.7ppm -623.7656 1586.4 y12-NH3^2/18.8ppm,y12-H2O+i^2/3.8ppm -632.2682 9946.8 y12^2/1.7ppm -632.7701 6533.9 y12+i^2/2.5ppm -633.2712 1699.8 y12+2i^2/3.5ppm -633.3458 2821.6 ? -634.7709 1205.1 b14-H2O^2/1.7ppm -644.2333 1023.6 ? -644.3076 878.1 ? -647.3327 849.1 ? -651.3581 8999.6 a8/1.3ppm -652.3618 3348.4 a8+i/2.7ppm -655.2262 2820.6 ? -660.3223 1516.4 y6-H2O/3.6ppm -661.3433 7606.5 b8-H2O/2.5ppm -662.3483 1380.0 b8-H2O+i/5.9ppm -667.2252 1019.2 ? -671.2955 1260.0 y13-H2O-NH3^2/7.3ppm -673.2364 4309.7 ? -674.2409 1688.8 ? -678.331 8546.4 y6/0.8ppm -679.2707 1080.4 ? -679.3559 8766.1 b8/5.4ppm -679.8054 1687.8 y13-H2O^2/2.2ppm -680.3547 2791.2 b8+i/-0.4ppm -681.2847 1116.1 ? -681.3271 1145.8 ? -685.2344 1975.1 ? -688.8099 8557.9 y13^2/1.1ppm -689.3101 7798.1 y13+i^2/-0.7ppm -689.8142 1742.5 y13+2i^2/4.4ppm -691.1587 1303.4 ? -699.2916 2484.3 ? -707.2698 3527.4 ? -708.3794 1450.8 a9/0.9ppm -715.3156 1258.6 y14-H2O^2/-9.6ppm -717.2615 3144.1 ? -723.9021 865.2 ? -724.2491 3238.7 ? -724.3282 4615.4 y14^2/0.7ppm -724.8292 4285.8 y14+i^2/0.1ppm -725.333 1740.7 y14+2i^2/4.4ppm -727.2462 3281.9 ? -728.2467 1480.9 ? -736.3738 7438.2 b9/0.2ppm -737.3769 2791.2 b9+i/0.7ppm -742.2589 5818.1 ? -742.3272 968.1 ? - diff --git a/implementations/python/examples/draw_entry.py b/implementations/python/examples/draw_entry.py deleted file mode 100644 index 8126d7e..0000000 --- a/implementations/python/examples/draw_entry.py +++ /dev/null @@ -1,27 +0,0 @@ -import sys -import matplotlib -matplotlib.use("agg") - -from matplotlib import pyplot as plt - -from mzlib.spectrum_library import SpectrumLibrary -from mzlib.draw import draw_spectrum - - -def main(path, spectrum_key): - lib = SpectrumLibrary(filename=path) - spec = lib.get_spectrum(spectrum_number=spectrum_key) - draw_spectrum(spec) - plt.savefig(f"{path}.{spectrum_key}.annotated.pdf", bbox_inches='tight') - - -if __name__ == '__main__': - try: - path = sys.argv[1] - index = sys.argv[2] - main(path, int(index)) - sys.exit(0) - except (IndexError, TypeError): - print("USAGE: ") - print("\tWrites the annotated spectrum to ..annotated.pdf") - sys.exit(1) diff --git a/implementations/python/examples/first_n_entries.py b/implementations/python/examples/first_n_entries.py deleted file mode 100644 index 0aa4c05..0000000 --- a/implementations/python/examples/first_n_entries.py +++ /dev/null @@ -1,42 +0,0 @@ -import click - -from mzlib import SpectrumLibrary -from mzlib.backends import SpectralLibraryBackendBase, FormatInferenceFailure, TextSpectralLibraryWriter -from mzlib.cluster import SpectrumCluster -from mzlib.index import MemoryIndex, SQLIndex -from mzlib.spectrum import Spectrum - -@click.command('first_n_entries') -@click.argument('inpath', type=click.Path(exists=True)) -@click.option("-i", "--input-format", type=click.Choice(sorted(SpectralLibraryBackendBase._file_extension_to_implementation)), - default=None) -@click.option("-n", '--spectra-to-read', type=int, default=20) -def main(inpath, input_format, spectra_to_read: int=20): - if SQLIndex.exists(inpath): - index_type = SQLIndex - else: - index_type = MemoryIndex - click.echo(f"Opening {inpath}", err=True) - try: - library = SpectrumLibrary(filename=inpath, index_type=index_type, format=input_format) - except FormatInferenceFailure as err: - click.echo(f"{err}", err=True) - raise click.Abort() - - stream = click.get_text_stream('stdout') - writer = TextSpectralLibraryWriter(stream) - writer.write_header(library) - - for i, entry in enumerate(library, 1): - if i > spectra_to_read: - break - if isinstance(entry, Spectrum): - writer.write_spectrum(entry) - elif isinstance(entry, SpectrumCluster): - writer.write_cluster(entry) - - writer.close() - - -if __name__ == "__main__": - main.main() \ No newline at end of file diff --git a/implementations/python/examples/massivekb_human_speclib_3cac03860ff7453a821332ab4cff20f4_head.sptxt b/implementations/python/examples/massivekb_human_speclib_3cac03860ff7453a821332ab4cff20f4_head.sptxt deleted file mode 100644 index 9a3f6b1..0000000 --- a/implementations/python/examples/massivekb_human_speclib_3cac03860ff7453a821332ab4cff20f4_head.sptxt +++ /dev/null @@ -1,6322 +0,0 @@ -Name: AAPSPSGGGGSGGGSGSGTPGPVGSPAPGHPAVSSMQGK/3 -Comment: Parent=1248.622192382813 Mods=2/0,A,Acetyl/38,K,TMT -Num peaks: 23 -230.17042541503906 4254.706615621117 "?" -248.18093872070312 7064.508902427105 "?" -298.11468505859375 1067.836646805394 "?" -369.17681884765625 1176.8354014799786 "?" -376.27606201171875 2337.4440043845175 "?" -433.2968444824219 3345.7398035088295 "?" -561.3554077148438 1737.1343610991503 "?" -692.3972778320312 1046.8388437553808 "?" -779.4280395507812 2207.9633842181515 "?" -866.4605102539062 3693.2327372695604 "?" -867.462646484375 1259.3862759802005 "?" -892.510009765625 1351.43676545469 "?" -965.5297241210938 1597.2180939099794 "?" -1036.5648193359375 1372.6161608370114 "?" -1082.0933837890625 1009.532530386963 "?" -1133.61865234375 10000.0 "?" -1134.6207275390625 4319.151225326226 "?" -1158.6256103515625 2871.9014810935946 "?" -1159.1282958984375 3242.6999497886145 "?" -1183.638916015625 2167.9284754234536 "?" -1424.7509765625 2746.137880049007 "?" 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tests/test_data/chinese_hamster_hcd_selected_head.msp tests/test_data/chinese_hamster_hcd_selected_head.mzlb.txt - mzspeclib convert -f json tests/test_data/chinese_hamster_hcd_selected_head.msp tests/test_data/chinese_hamster_hcd_selected_head.mzlb.json - mzspeclib convert -f json "tests/test_data/complex_interpretations_with_members.mzlb.txt" tests/test_data/complex_interpretations_with_members.mzlb.json - python tests/test_data/generate_annotations.py - mzspeclib convert -f text examples/chinese_hamster_hcd_selected_head.msp examples/chinese_hamster_hcd_selected_head.mzlb.txt \ No newline at end of file diff --git a/implementations/python/mzlib/__init__.py b/implementations/python/mzlib/__init__.py deleted file mode 100644 index 65badd8..0000000 --- a/implementations/python/mzlib/__init__.py +++ /dev/null @@ -1,11 +0,0 @@ -"""HUPO-PSI Spectral library format.""" - -from mzlib.spectrum import Spectrum -from mzlib.analyte import Analyte, Interpretation - -from mzlib.index import MemoryIndex, SQLIndex - -from mzlib.spectrum_library import SpectrumLibrary -from mzlib.spectrum_library_index import SpectrumLibraryIndex -from mzlib.spectrum_library_collection import SpectrumLibraryCollection -from mzlib.universal_spectrum_identifier import UniversalSpectrumIdentifier diff --git a/implementations/python/mzlib/analyte.py b/implementations/python/mzlib/analyte.py deleted file mode 100644 index a53df52..0000000 --- a/implementations/python/mzlib/analyte.py +++ /dev/null @@ -1,233 +0,0 @@ -import warnings - -try: - from collections.abc import (MutableMapping, Mapping) -except ImportError: - from collections import (MutableMapping, Mapping) - -from typing import Iterable, KeysView, ItemsView, Optional, ValuesView, Dict - -from pyteomics import proforma - -from mzlib.attributes import AttributedEntity, IdentifiedAttributeManager, AttributeManagedProperty, AttributeProxy, AttributeGroupFacet - - -FIRST_ANALYTE_KEY = '1' -FIRST_INTERPRETATION_KEY = '1' - -ANALYTE_MIXTURE_TERM = "MS:1003163|analyte mixture members" -CHARGE_STATE = "MS:1000041|charge state" -PROFORMA_ION = "MS:1003270|proforma peptidoform ion notation" -PROFORMA_SEQ = "MS:1000889|proforma peptidoform sequence" - - -class _AnalyteMappingProxy(Mapping): - parent: Mapping - - def __init__(self, parent): - self.parent = parent - - def __getitem__(self, key): - for group_id, group in self.parent.items(): - if key in group: - return group[key] - raise KeyError(key) - - def __iter__(self): - keys = set() - for group_id, group in self.parent.items(): - k_ = set(group.keys()) - keys.update(k_) - return iter(keys) - - def __len__(self): - return sum([len(v) for v in self.parent.values()]) - - def __repr__(self): - d = dict(self) - return f"{self.__class__.__name__}({d})" - - -class InterpretationCollection(MutableMapping): - __slots__ = ('interpretations', ) - - interpretations: Dict[str, 'Interpretation'] - - def __init__(self, interpretations=None): - if interpretations is None: - interpretations = {} - self.interpretations = interpretations - - def get_interpretation(self, interpretation_id) -> 'Interpretation': - return self.interpretations[str(interpretation_id)] - - def add_interpretation(self, interpretation: 'Interpretation'): - self.set_interpretation(str(interpretation.id), interpretation) - - def set_interpretation(self, key, interpretation: 'Interpretation'): - self.interpretations[str(key)] = interpretation - - def __getitem__(self, key) -> 'Interpretation': - return self.get_interpretation(key) - - def __setitem__(self, key, value: 'Interpretation'): - self.set_interpretation(key, value) - - def __delitem__(self, key): - del self.interpretations[str(key)] - - def __len__(self): - return len(self.interpretations) - - def __contains__(self, key): - return key in self.interpretations - - def __iter__(self): - return iter(self.interpretations) - - def keys(self) -> KeysView[str]: - return self.interpretations.keys() - - def values(self) -> ValuesView['Interpretation']: - return self.interpretations.values() - - def items(self) -> ItemsView[str, 'Interpretation']: - return self.interpretations.items() - - @property - def analytes(self) -> '_AnalyteMappingProxy': - return _AnalyteMappingProxy(self) - - def __repr__(self): - d = dict(self) - return f"{self.__class__.__name__}({d})" - - -class Interpretation(AttributedEntity, MutableMapping): - __slots__ = ('id', 'analytes', 'member_interpretations') - - id: str - analytes: Dict[str, 'Analyte'] - member_interpretations: Dict[str, 'InterpretationMember'] - - def __init__(self, id, attributes: Iterable = None, analytes: Dict = None, member_interpretations: Dict = None): - self.id = str(id) - self.analytes = analytes or {} - self.member_interpretations = member_interpretations or {} - super(Interpretation, self).__init__(attributes) - - def _update_mixture_members_term(self): - value = sorted(map(int, self.analytes.keys())) - self.replace_attribute(ANALYTE_MIXTURE_TERM, value) - - def get_analyte(self, analyte_id) -> 'Analyte': - return self.analytes[str(analyte_id)] - - def add_analyte(self, analyte: 'Analyte'): - self.set_analyte(analyte.id, analyte) - self._update_mixture_members_term() - - def set_analyte(self, key, analyte: 'Analyte'): - self.analytes[str(key)] = analyte - self._update_mixture_members_term() - - def remove_analyte(self, analyte_id): - del self.analytes[str(analyte_id)] - self._update_mixture_members_term() - - def has_analyte(self, analyte_id) -> bool: - return str(analyte_id) in self.analytes - - def get_member_interpretation(self, member_id) -> 'InterpretationMember': - return self.member_interpretations[str(member_id)] - - def add_member_interpretation(self, interpretation_member: 'InterpretationMember'): - self.set_member_interpretation(interpretation_member.id, interpretation_member) - - def set_member_interpretation(self, key, interpretation_member: 'InterpretationMember'): - self.member_interpretations[str(key)] = interpretation_member - - def remove_member_interpretation(self, member_id): - del self.member_interpretations[str(member_id)] - - def validate(self) -> bool: - """ - Perform validation on each component to confirm this object is well formed. - - Returns - ------- - bool - """ - analyte_ids = set(self.analytes) - member_ids = set(self.member_interpretations) - valid = True - if not (analyte_ids >= member_ids): - warnings.warn( - f"Interpretation has InterpretationMembers {member_ids - analyte_ids} lacking Analytes") - valid = False - return valid - - def __getitem__(self, key) -> 'Analyte': - return self.get_analyte(key) - - def __setitem__(self, key, value: 'Analyte'): - self.set_analyte(key, value) - - def __delitem__(self, key): - self.remove_analyte(key) - - def __iter__(self): - return iter(self.analytes) - - def __len__(self): - return len(self.analytes) - - def __repr__(self): - d = dict(self) - a = '' - if self.attributes: - a = f', {self.attributes}' - return f"{self.__class__.__name__}({d}{a})" - - -class InterpretationMember(IdentifiedAttributeManager): - __slots__ = () - - -class ProteinDescription(AttributeProxy): - accession = AttributeManagedProperty("MS:1000885|protein accession") - name = AttributeManagedProperty("MS:1000886|protein name") - missed_cleavages = AttributeManagedProperty[int]("MS:1003044|number of missed cleavages") - cleavage_agent = AttributeManagedProperty("MS:1001045|cleavage agent name") - number_of_enzymatic_termini = AttributeManagedProperty[int]("MS:1003048|number of enzymatic termini") - flanking_n_terminal_residue = AttributeManagedProperty("MS:1001112|n-terminal flanking residue") - flanking_c_terminal_residue = AttributeManagedProperty("MS:1001113|c-terminal flanking residue") - - -class Analyte(IdentifiedAttributeManager): - __slots__ = () - - mass = AttributeManagedProperty[float]("MS:1001117|theoretical mass") - peptide = AttributeManagedProperty[str]("MS:1003169|proforma peptidoform sequence") - proteins = AttributeGroupFacet[ProteinDescription](ProteinDescription) - - @property - def charge(self) -> Optional[int]: - if self.has_attribute(CHARGE_STATE): - return self.get_attribute(CHARGE_STATE) - elif self.has_attribute(PROFORMA_ION): - ion_val = self.get_attribute(PROFORMA_ION) - val = proforma.ProForma.parse(ion_val) - return val.charge_state - else: - return None - - @charge.setter - def charge(self, value): - if value is not None: - if self.has_attribute(CHARGE_STATE): - self.replace_attribute(CHARGE_STATE, value) - else: - self.add_attribute(CHARGE_STATE, value) - else: - self.remove_attribute(CHARGE_STATE) \ No newline at end of file diff --git a/implementations/python/mzlib/annotation.py b/implementations/python/mzlib/annotation.py deleted file mode 100644 index b5d7f99..0000000 --- a/implementations/python/mzlib/annotation.py +++ /dev/null @@ -1 +0,0 @@ -from mzpaf.annotation import * \ No newline at end of file diff --git a/implementations/python/mzlib/attributes.py b/implementations/python/mzlib/attributes.py deleted file mode 100644 index 6106fb1..0000000 --- a/implementations/python/mzlib/attributes.py +++ /dev/null @@ -1,827 +0,0 @@ -import textwrap - -from typing import ( - Any, DefaultDict, Iterable, - Iterator, Optional, Set, Tuple, - Union, List, Dict, - Generic, TypeVar, Type -) - - -T = TypeVar('T') - - -class Attribute(object): - __slots__ = ("key", "value", "group_id", "owner_id") - key: str - value: Union[str, int, float, 'Attribute', List] - group_id: Optional[str] - owner_id: int - - def __init__(self, key, value, group_id=None, owner_id=-1): - self.key = key - self.value = value - self.group_id = group_id - self.owner_id = owner_id - - def copy(self): - return self.__class__(self.key, self.value, self.group_id, self.owner_id) - - def __getitem__(self, i): - if i == 0: - return self.key - elif i == 1: - return self.value - elif i == 2: - return self.group_id - elif i == 3: - return self.owner_id - else: - raise IndexError(i) - - def __iter__(self): - yield self.key - yield self.value - if self.group_id: - yield self.group_id - yield self.owner_id - - def __len__(self): - if self.group_id is None: - return 2 - return 3 - - def __eq__(self, other): - if other is None: - return False - return self.key == other.key and self.value == other.value and self.group_id == other.group_id - - def __ne__(self, other): - return not self == other - - def __repr__(self): - return f"{self.__class__.__name__}({self.key}, {self.value}, {self.group_id})" - - def __str__(self): - base = f"{self.key}={self.value}" - if self.group_id: - base = f"[{self.group_id}]" + base - return base - - def __hash__(self): - key = (self.key, ) - if self.group_id is not None: - key = (self.key, self.group_id) - return hash(key) - - -class AttributeManager(object): - """ - A key-value pair store with optional attribute grouping - - Attributes - ---------- - attributes: List[List] - The actual attribute name-value pairs with an optional grouping value - attribute_dict: Dict - A mapping from attribute name to indices into :attr:`attributes` and - the group assignments. - group_dict: Dict - A mapping from group identifier to indices into :attr:`attributes` - group_counter: int - The number of attribute groups assigned. - - """ - - attributes: List[Attribute] - attribute_dict: Dict - group_dict: Dict - group_counter: int - - - __slots__ = ('attributes', 'attribute_dict', 'group_dict', 'group_counter') - - def __init__(self, attributes: Iterable = None): - """ - - Parameters - ---------- - attributes : Iterable[list], optional - Attribute name-value pairs with an optional grouping value. If omitted, - the attribute store will be empty. - """ - self.attributes = [] - - # Internal index attributes - self.attribute_dict = {} - self.group_dict = {} - self.group_counter = 1 - if attributes is not None: - self._from_iterable(attributes) - - def get_next_group_identifier(self) -> str: - """ - Retrieve the next un-used attribute group identifier - and increment the internal counter. - - Returns - ------- - str - """ - next_value = self.group_counter - self.group_counter += 1 - return str(next_value) - - #### Add an attribute to the list and update the lookup tables - def add_attribute(self, key: str, value, group_identifier: Optional[str] = None): - """ - Add an attribute to the list and update the lookup tables - - Parameters - ---------- - key : str - The name of the attribute to add - value : object - The value of the attribute to add - group_identifier : str, optional - The attribute group identifier to use, if any. If not provided, - no group is assumed. - """ - if group_identifier is not None: - int_group_identifier = int(group_identifier) - if int_group_identifier <= self.group_counter: - self.group_counter = int_group_identifier + 1 - items = Attribute(key, value, group_identifier) - self.attributes.append(items) - index = len(self.attributes) - 1 - - #### If there is already one of these, add it to the lists in attribute_dict - if key in self.attribute_dict: - self.attribute_dict[key]["indexes"].append(index) - if group_identifier is not None: - self.attribute_dict[key]["groups"].append(group_identifier) - - #### Otherwise, create the entry in attribute_dict - else: - if group_identifier is not None: - self.attribute_dict[key] = {"indexes": [ - index], "groups": [group_identifier]} - else: - self.attribute_dict[key] = {"indexes": [index], "groups": []} - - #### If there is a group_identifier, then update the group_dict - if group_identifier is not None: - #### If this group already has one or more entries, add to it - if group_identifier in self.group_dict: - self.group_dict[group_identifier].append(index) - #### Else create and entry for the group_identifier - else: - self.group_dict[group_identifier] = [index] - - def add_attribute_group(self, attributes: List[Union[Attribute, Tuple[str, Any]]]): - group_id = self.get_next_group_identifier() - for attr in attributes: - if isinstance(attr, Attribute): - key = attr.key - value = attr.value - else: - key, value = attr - self.add_attribute(key, value, group_id) - - def get_attribute(self, key: str, group_identifier: Optional[str] = None, - raw: bool = False) -> Union[Any, List[Any], Attribute, - List[Attribute]]: - """ - Get the value or values associated with a given - attribute key. - - Parameters - ---------- - key : str - The name of the attribute to retrieve - group_identifier : str, optional - The specific group identifier to return from. - raw : bool - Whether to return the :class:`Attribute` object or unwrap the value - - Returns - ------- - attribute_value: object or list[object] - Returns single or multiple values for the requested attribute. - """ - indices_and_groups = self.attribute_dict[key] - if group_identifier is None: - indices = indices_and_groups['indexes'] - if len(indices) > 1: - if raw: - return [self.attributes[i] for i in indices] - return [self.attributes[i][1] for i in indices] - else: - if raw: - return self.attributes[indices[0]] - return self.attributes[indices[0]][1] - else: - groups = indices_and_groups['groups'] - try: - i = groups.index(group_identifier) - except ValueError: - raise KeyError(f"Group {group_identifier} not found") from None - indices = indices_and_groups['indexes'] - idx = indices[i] - if raw: - return self.attributes[idx] - return self.attributes[idx][1] - - def get_attribute_group(self, group_identifier: str) -> List[Any]: - result = [] - group_identifier = str(group_identifier) - for k, indices_and_groups in self.attribute_dict.items(): - for i, g in zip(indices_and_groups['indexes'], indices_and_groups['groups']): - if g == group_identifier: - result.append(self.attributes[i]) - return result - - def replace_attribute(self, key, value, group_identifier=None): - try: - indices_and_groups = self.attribute_dict[key] - except KeyError: - return self.add_attribute(key, value, group_identifier=group_identifier) - if group_identifier is None: - indices = indices_and_groups['indexes'] - if len(indices) > 1: - raise ValueError("Cannot replace the value of an attribute used multiple times") - else: - self.attributes[indices[0]].value = value - else: - raise NotImplementedError() - - def get_by_name(self, name: str): - """ - Search for an attribute by human-readable name. - - Parameters - ---------- - name: str - The name to search for. - - Returns - ------- - object: - The attribute value if found or :const:`None`. - """ - matches = [] - for attr in self: - if attr.key.split("|")[-1] == name: - matches.append(attr[1]) - n = len(matches) - if n == 1: - return matches[0] - elif n > 1: - return matches - return None - - def clear(self): - """Remove all content from the store.""" - self._clear_attributes() - - def remove_attribute(self, key, group_identifier=None): - """ - Remove the value or values associated with a given - attribute key from the store. - - This rebuilds the entire store, which may be expensive. - - Parameters - ---------- - key : str - The name of the attribute to retrieve - group_identifier : str, optional - The specific group identifier to return from. - - """ - indices_and_groups = self.attribute_dict[key] - if group_identifier is None: - indices = indices_and_groups['indexes'] - if len(indices) > 1: - indices = sorted(indices, reverse=True) - for i in indices: - self.attributes.pop(i) - else: - self.attributes.pop(indices[0]) - else: - groups = indices_and_groups['groups'] - i = groups.index(group_identifier) - indices = indices_and_groups['indexes'] - idx = indices[i] - self.attributes.pop(idx) - attributes = self.attributes - self.clear() - self._from_iterable(attributes) - - def _remove_attribute_group(self, group_identifier): - group_indices = self.group_dict.pop(group_identifier) - for offset, i in enumerate(sorted(group_indices)): - self.attributes.pop(i - offset) - attributes = self.attributes - self.clear() - self._from_iterable(attributes) - - def _iter_attribute_groups(self): - seen = set() - for group_id, indices in self.group_dict.items(): - yield group_id, [self.attributes[i] for i in indices] - seen.update(indices) - acc = [] - for i, attr in enumerate(self.attributes): - if i in seen: - continue - acc.append(attr) - yield None, acc - - def has_attribute(self, key): - """ - Test for the presence of a given attribute - - Parameters - ---------- - key : str - The attribute to test for - - Returns - ------- - bool - """ - return key in self.attribute_dict - - def __contains__(self, key): - return self.has_attribute(key) - - def __getitem__(self, key): - return self.get_attribute(key) - - def __setitem__(self, key, value): - if self.has_attribute(key): - self.replace_attribute(key, value) - else: - self.add_attribute(key, value) - - def keys(self): - return self.attribute_dict.keys() - - def __eq__(self, other): - if other is None: - return False - self_keys = self.keys() - other_keys = other.keys() - if len(self_keys) != len(other_keys): - return False - for key in self_keys: - try: - self_value = self.get_attribute(key) - other_value = other.get_attribute(key) - except KeyError: - return False - if self_value != other_value: - return False - return True - - def __ne__(self, other): - return not self == other - - def __len__(self): - return self._count_attributes() - - def __bool__(self): - return len(self) > 0 - - def __iter__(self): - return self._iter_attributes() - - def _count_attributes(self) -> int: - return len(self.attributes) - - def _iter_attributes(self) -> Iterator[Attribute]: - return iter(self.attributes) - - def _clear_attributes(self): - self.attributes = [] - - # Internal index attributes - self.attribute_dict = {} - self.group_dict = {} - self.group_counter = 1 - - def _from_iterable(self, attributes): - mapping = {} - for attrib in attributes: - if len(attrib) == 3: - # this is a grouped attribute - if attrib[2] in mapping: - remap = mapping[attrib[2]] - else: - remap = self.get_next_group_identifier() - mapping[attrib[2]] = remap - self.add_attribute(attrib[0], attrib[1], remap) - else: - self.add_attribute(attrib[0], attrib[1]) - - def _attributes_from_iterable(self, attributes): - return self._from_iterable(attributes) - - def copy(self): - """Make a deep copy of the object""" - return self.__class__(self.attributes) - - def __repr__(self): - if len(self) == 0: - return f"{self.__class__.__name__}([])" - lines = list(map(str, self.attributes)) - template = "{}([\n{}])" - return template.format( - self.__class__.__name__, - textwrap.indent(',\n'.join(lines), ' ' * 2)) - - -class IdentifiedAttributeManager(AttributeManager): - __slots__ = ('id', ) - - id: str - - def __init__(self, id, attributes: Iterable = None): - self.id = str(id) - super(IdentifiedAttributeManager, self).__init__(attributes) - - def __repr__(self): - template = f"{self.__class__.__name__}(id={self.id}, " - lines = list(map(str, self.attributes)) - if not lines: - template += "[])" - return template - template += "[\n%s])" % textwrap.indent(',\n'.join(lines), ' ' * 2) - return template - - -class _ReadAttributes(object): - __slots__ = () - - attributes: AttributeManager - - def get_attribute(self, key, group_identifier=None, raw: bool = False): - """ - Get the value or values associated with a given - attribute key from the entity's attribute store. - - Parameters - ---------- - key : str - The name of the attribute to retrieve - group_identifier : str, optional - The specific group identifier to return from. - raw : bool, optional - To return the stored value, or an :class:`Attribute` object preserving - additional information - - Returns - ------- - attribute_value: object or list[object] - Returns single or multiple values for the requested attribute. - """ - return self.attributes.get_attribute(key, group_identifier=group_identifier, raw=raw) - - def get_attribute_group(self, group_identifier: str) -> List[Any]: - return self.attributes.get_attribute_group(group_identifier) - - def has_attribute(self, key) -> bool: - """ - Test for the presence of a given attribute in the library - level store. - - Parameters - ---------- - key : str - The attribute to test for - - Returns - ------- - bool - """ - return self.attributes.has_attribute(key) - - def get_by_name(self, name: str): - """ - Search for an attribute by human-readable name. - - Parameters - ---------- - name: str - The name to search for. - - Returns - ------- - object: - The attribute value if found or :const:`None`. - """ - return self.attributes.get_by_name(name) - - def _iter_attribute_groups(self): - return self.attributes._iter_attribute_groups() - - def _count_attributes(self) -> int: - return self.attributes._count_attributes() - - def _iter_attributes(self) -> Iterator[Attribute]: - return self.attributes._iter_attributes() - - -class _WriteAttributes(object): - __slots__ = () - - attributes: AttributeManager - - def add_attribute(self, key, value, group_identifier=None) -> Union[Any, List[Any]]: - """ - Add an attribute to the entity's attributes store. - - Parameters - ---------- - key : str - The name of the attribute to add - value : object - The value of the attribute to add - group_identifier : str, optional - The attribute group identifier to use, if any. If not provided, - no group is assumed. - """ - return self.attributes.add_attribute(key, value, group_identifier=group_identifier) - - def add_attribute_group(self, attributes: List[Union[Attribute, Tuple[str, Any]]]): - self.attributes.add_attribute_group(attributes) - - def replace_attribute(self, key, value, group_identifier=None): - return self.attributes.replace_attribute(key, value, group_identifier=group_identifier) - - def remove_attribute(self, key, group_identifier=None): - """ - Remove the value or values associated with a given - attribute key from the entity's attribute store. - - This rebuilds the entire store, which may be expensive. - - Parameters - ---------- - key : str - The name of the attribute to retrieve - group_identifier : str, optional - The specific group identifier to return from. - - """ - return self.attributes.remove_attribute(key, group_identifier=group_identifier) - - def _attributes_from_iterable(self, attributes): - return self.attributes._attributes_from_iterable(attributes) - - def _clear_attributes(self): - return self.attributes._clear_attributes() - - -class AttributedEntity(_ReadAttributes, _WriteAttributes): - """ - A base type for entities which contain an :class:`AttributeManager` - without being completely subsumed by it. - - An :class:`AttributeManager` represents a collection of attributes - first and foremost, supplying :class:`~.collections.abc.MutableMapping`-like - interface to them, in addition to methods. - """ - - __slots__ = ("attributes", ) - - attributes: AttributeManager - - def __init__(self, attributes: Iterable=None, **kwargs): - self.attributes = AttributeManager(attributes) - super().__init__(**kwargs) - - -Attributed = Union[AttributeManager, AttributedEntity] - - -class AttributeManagedProperty(Generic[T]): - __slots__ = ("attribute", "multiple") - attribute: str - multiple: bool - - def __init__(self, attribute: str, multiple: bool = False): - self.attribute = attribute - self.multiple = multiple - - def _get_group_id(self, inst: AttributeManager) -> Optional[str]: - return getattr(inst, "group_id", None) - - def __get__(self, inst: AttributeManager, cls: Type) -> T: - if inst is None: - return self - if inst.has_attribute(self.attribute): - value = inst.get_attribute(self.attribute, group_identifier=self._get_group_id(inst)) - if self.multiple and not isinstance(value, list): - value = [value] - return value - return None - - def __set__(self, inst: AttributeManager, value: T): - attrib = self.attribute - if inst.has_attribute(attrib): - inst.replace_attribute(attrib, value, group_identifier=self._get_group_id(inst)) - elif inst._count_attributes() > 0: - attribs = [[attrib, value]] + list(inst._iter_attributes()) - inst._clear_attributes() - inst._attributes_from_iterable(attribs) - else: - inst.add_attribute(attrib, value, group_identifier=self._get_group_id(inst)) - - def __delete__(self, inst: AttributeManager, attr): - inst.remove_attribute(self.attribute, group_identifier=self._get_group_id(inst)) - - -class AttributeListManagedProperty(Generic[T]): - __slots__ = ("attributes", ) - attributes: List[str] - - def __init__(self, attributes: List[str]): - self.attributes = attributes - - def __get__(self, inst: AttributeManager, cls: Type) -> T: - if inst is None: - return self - key, val = self._find_key_used(inst) - return val - - def _find_key_used(self, inst: AttributeManager) -> Optional[Tuple[str, T]]: - for attr in self.attributes: - try: - return attr, inst.get_attribute(attr) - except KeyError: - continue - return None, None - - def __set__(self, inst: AttributeManager, value: T): - key, _val = self._find_key_used(inst) - if key is None: - attrib = self.attributes[0] - else: - attrib = key - if inst.has_attribute(attrib): - inst.replace_attribute(attrib, value) - elif inst._count_attributes() > 0: - attribs = [[attrib, value]] + list(inst._iter_attributes()) - inst._clear_attributes() - inst._attributes_from_iterable(attribs) - else: - inst.add_attribute(attrib, value) - - def __delete__(self, inst: AttributeManager, attr): - key, val = self._find_key_used(inst) - if key is not None: - inst.remove_attribute(key) - - -class AttributeProxyMeta(type): - def __new__(cls, typename, bases, namespace): - props = {} - for k, v in namespace.items(): - if isinstance(v, (AttributeManagedProperty, AttributeListManagedProperty)): - props[k] = v - for base in bases[::-1]: - if hasattr(base, '_attribute_props'): - for k, v in base._attribute_props.items(): - if k not in props: - props[k] = v - namespace['_attribute_props'] = props - if "__repr__" not in namespace: - def __repr__(self): - pairs = [] - for k in self._attribute_props: - try: - value = getattr(self, k) - except KeyError: - value = None - pairs.append((k, value)) - content = ', '.join(f"{k}={v!r}" for k, v in pairs) - return f"{self.__class__.__name__}({content})" - namespace['__repr__'] = __repr__ - return super().__new__(cls, typename, bases, namespace) - - -class ROAttributeProxy(_ReadAttributes, metaclass=AttributeProxyMeta): - attributes: Attributed - - def __init__(self, attributes): - self.attributes = attributes - - -AttributeProxy = ROAttributeProxy - - -class AttributeSet(AttributedEntity): - name: str - _names_to_override: Set[str] - - def __init__(self, name: str, attributes: Iterable = None, **kwargs): - super().__init__(attributes, **kwargs) - self.name = name - self._names_to_override = self._get_names_to_override() - - def _get_names_to_override(self): - keys = set() - for attr in self.attributes: - if attr.group_id is None: - keys.add(attr.key) - return keys - - def member_of(self, target: Attributed) -> bool: - for attrib in self.attributes: - if attrib.group_id: - raise NotImplementedError() - if not target.has_attribute(attrib.key): - return False - return True - - def apply(self, target: Attributed): - - terms_to_remove: List[Tuple[str, Union[Attribute, List[Attribute]]]] = [] - for key in self.attributes.keys(): - if target.has_attribute(key): - terms_to_remove.append((key, target.get_attribute(key, raw=True))) - - group_ids = DefaultDict(int) - for key, terms in terms_to_remove: - if isinstance(terms, list): - for term in terms: - if term.group_id: - group_ids[term.group_id] += 1 - target.remove_attribute(key, group_identifier=term.group_id) - else: - if term.group_id: - group_ids[term.group_id] += 1 - target.remove_attribute(key, group_identifier=term.group_id) - - for group_id in group_ids: - target._remove_attribute_group(group_id) - - for group_id, attrs in self._iter_attribute_groups(): - if group_id is None: - for a in attrs: - target.add_attribute(a.key, a.value, group_identifier=None) - else: - target.add_attribute_group(attrs) - - def __repr__(self): - template = f"{self.__class__.__name__}(name={self.name}, " - lines = list(map(str, self.attributes)) - if not lines: - template += "[])" - return template - template += "[\n%s])" % textwrap.indent(',\n'.join(lines), ' ' * 2) - return template - - -class AttributeFacet(Generic[T]): - facet_type: Type[T] - - def __init__(self, facet_type: Type[T]): - self.facet_type = facet_type - - def __get__(self, inst: Attributed, klass: Type[Attributed]) -> T: - if inst is not None: - return self.facet_type(inst) - else: - return self - - -class AttributeGroupFacet(Generic[T]): - facet_type: Type[T] - - def __init__(self, facet_type: Type[T]): - self.facet_type = facet_type - - def wraps(self, attributed: Attributed) -> List[T]: - attribute_groups = [] - facet_keys = {a.attribute for a in self.facet_type._attribute_props.values()} - for group_id in attributed.group_dict: - group = attributed.get_attribute_group(group_id) - group_keys = {a.key for a in group} - if group_keys & facet_keys: - attribute_groups.append(group_id) - - facets = [] - for group_id in attribute_groups: - facet = self.facet_type(attributed) - facet.group_id = group_id - facets.append(facet) - return facets - - def __get__(self, inst: Attributed, klass) -> Union[List[T], 'AttributeGroupFacet']: - if inst is not None: - return self.wraps(inst) - return self - diff --git a/implementations/python/mzlib/backends/__init__.py b/implementations/python/mzlib/backends/__init__.py deleted file mode 100644 index 1e6faec..0000000 --- a/implementations/python/mzlib/backends/__init__.py +++ /dev/null @@ -1,8 +0,0 @@ -from .text import TextSpectralLibrary, TextSpectralLibraryWriter -from .json import JSONSpectralLibrary, JSONSpectralLibraryWriter -from .msp import MSPSpectralLibrary -from .bibliospec import BibliospecSpectralLibrary -from .sptxt import SPTXTSpectralLibrary -from .diann import DiaNNTSVSpectralLibrary, DIANNTSVSpectralLibrary -from .spectronaut import SpectronautTSVSpectralLibrary -from .base import (guess_implementation, SpectralLibraryBackendBase, SpectralLibraryWriterBase, FormatInferenceFailure) \ No newline at end of file diff --git a/implementations/python/mzlib/backends/base.py b/implementations/python/mzlib/backends/base.py deleted file mode 100644 index 00d9669..0000000 --- a/implementations/python/mzlib/backends/base.py +++ /dev/null @@ -1,702 +0,0 @@ -import io -import csv -import enum -import logging -import warnings - -from typing import Any, Callable, Dict, Iterable, Union, List, Type, Iterator -from pathlib import Path - - -from psims.controlled_vocabulary import Entity -from psims.controlled_vocabulary.controlled_vocabulary import ( - load_uo, load_unimod, load_psims) -from mzlib.cluster import SpectrumCluster - -from mzlib.index import MemoryIndex, SQLIndex, IndexBase -from mzlib.spectrum import LIBRARY_SPECTRUM_INDEX, LIBRARY_SPECTRUM_KEY, Spectrum -from mzlib.analyte import Analyte, Interpretation, InterpretationMember, ANALYTE_MIXTURE_TERM -from mzlib.attributes import Attributed, AttributedEntity, AttributeSet, AttributeManagedProperty -from mzlib.ontology import _VocabularyResolverMixin - -from .utils import open_stream, _LineBuffer - -logger = logging.getLogger(__name__.rsplit(".", 1)[0]) -logger.addHandler(logging.NullHandler()) - -ANALYTE_MIXTURE_CURIE = ANALYTE_MIXTURE_TERM.split("|")[0] - -FORMAT_VERSION_TERM = 'MS:1003186|library format version' -LIBRARY_NAME_TERM = "MS:1003188|library name" -LIBRARY_VERSION_TERM = "MS:1003190|library version" -LIBRARY_IDENTIFIER_TERM = "MS:1003187|library identifier" -LIBRARY_DESCRIPTION_TERM = "MS:1003189|library description" -LIBRARY_URI_TERM = "MS:1003191|library URI" - - -DEFAULT_VERSION = '1.0' - - -class AttributeSetTypes(enum.Enum): - spectrum = enum.auto() - analyte = enum.auto() - interpretation = enum.auto() - cluster = enum.auto() - - -class FormatInferenceFailure(ValueError): - """Indicates that we failed to infer the format type for a spectral library.""" - - -class SubclassRegisteringMetaclass(type): - def __new__(mcs, name, parents, attrs): - new_type = type.__new__(mcs, name, parents, attrs) - if not hasattr(new_type, "_file_extension_to_implementation"): - new_type._file_extension_to_implementation = dict() - - file_extension = attrs.get("file_format") - if file_extension is not None: - if isinstance(file_extension, list): - for ext in file_extension: - new_type._file_extension_to_implementation[ext] = new_type - else: - new_type._file_extension_to_implementation[file_extension] = new_type - - format_name = attrs.get("format_name") - if format_name is not None: - new_type._file_extension_to_implementation[format_name] = new_type - else: - attrs['format_name'] = file_extension - return new_type - - def type_for_format(cls, format_or_extension): - return cls._file_extension_to_implementation.get(format_or_extension) - - -class _LibraryViewMixin: - - name = AttributeManagedProperty[str](LIBRARY_NAME_TERM) - identifier = AttributeManagedProperty[str](LIBRARY_IDENTIFIER_TERM) - description = AttributeManagedProperty[str](LIBRARY_DESCRIPTION_TERM) - uri = AttributeManagedProperty[str](LIBRARY_URI_TERM) - library_version = AttributeManagedProperty[str](LIBRARY_VERSION_TERM) - - @property - def format_version(self): - try: - value = self.get_attribute(FORMAT_VERSION_TERM) - return value - except KeyError: - value = DEFAULT_VERSION - self.add_attribute(FORMAT_VERSION_TERM, value) - return value - - -class SpectralLibraryBackendBase(AttributedEntity, _VocabularyResolverMixin, _LibraryViewMixin, metaclass=SubclassRegisteringMetaclass): - """A base class for all spectral library formats.""" - - file_format = None - - _file_extension_to_implementation: Dict[str, - Type['SpectralLibraryBackendBase']] = {} - _format_name_to_implementation: Dict[str, - Type['SpectralLibraryBackendBase']] = {} - - index: IndexBase - - spectrum_attribute_sets: Dict[str, AttributeSet] - analyte_attribute_sets: Dict[str, AttributeSet] - interpretation_attribute_sets: Dict[str, AttributeSet] - cluster_attribute_sets: Dict[str, AttributeSet] - - @classmethod - def guess_from_filename(cls, filename: Union[str, Path, io.FileIO]) -> bool: - """ - Guess if the file is of this type by inspecting the file's name and extension. - - Parameters - ---------- - filename : str - The path to the file to inspect. - - Returns - ------- - bool: - Whether this is an appropriate backend for that file. - """ - if hasattr(filename, "name"): - filename = filename.name - if not isinstance(filename, (str, Path)): - return False - if filename.endswith(".gz"): - filename = filename[:-3] - if isinstance(cls.file_format, list): - return any(filename.endswith(ext) for ext in cls.file_format) - return filename.endswith(cls.file_format) - - @classmethod - def guess_from_header(cls, filename: Union[str, Path, io.FileIO]) -> bool: - """ - Guess if the file is of this type by inspecting the file's header section - - Parameters - ---------- - filename : str - The path to the file to open. - - Returns - ------- - bool: - Whether this is an appropriate backend for that file. - """ - return False - - @classmethod - def guess_implementation(cls, filename: Union[str, Path, io.FileIO], index_type=None, - **kwargs) -> 'SpectralLibraryBackendBase': - """ - Guess the backend implementation to use with this file format. - - Parameters - ---------- - filename : str - The path to the spectral library file to open. - index_type : type, optional - The :class:`~.IndexBase` derived type to use for this file. If - :const:`None` is provided, the instance will decide based upon - :meth:`has_index_preference`. - **kwargs - Passed to implementation - - Returns - ------- - SpectralLibraryBackendBase - """ - for key, impl in cls._file_extension_to_implementation.items(): - try: - if impl.guess_from_filename(filename): - return impl(filename, index_type=index_type, **kwargs) - except TypeError: - pass - try: - if impl.guess_from_header(filename): - return impl(filename, index_type=index_type, **kwargs) - except (TypeError, UnicodeDecodeError): - pass - raise FormatInferenceFailure(f"Could not guess backend implementation for {filename}") - - def __init__(self, filename: Union[str, Path, io.FileIO]): - self.filename = filename - self.index = MemoryIndex() - - self.spectrum_attribute_sets = { - "all": AttributeSet("all", []) - } - self.analyte_attribute_sets = { - "all": AttributeSet("all", []) - } - self.interpretation_attribute_sets = { - "all": AttributeSet("all", []) - } - self.cluster_attribute_sets = { - "all": AttributeSet("all", []) - } - - super().__init__(None) - - def read_header(self) -> bool: - """ - Read just the header of the whole library - - Returns - ------- - bool - """ - raise NotImplementedError() - - def _new_spectrum(self) -> Spectrum: - spec = Spectrum() - attr_set = self.spectrum_attribute_sets.get("all") - if attr_set: - attr_set.apply(spec) - return spec - - def _new_interpretation(self, id=None) -> Interpretation: - interp = Interpretation(id) - attr_set = self.interpretation_attribute_sets.get('all') - if attr_set: - attr_set.apply(interp) - return interp - - def _new_interpretation_member(self, id=None) -> InterpretationMember: - return InterpretationMember(id) - - def _new_analyte(self, id=None) -> Analyte: - analyte = Analyte(id) - attr_set = self.analyte_attribute_sets.get('all') - if attr_set: - attr_set.apply(analyte) - return analyte - - def _new_cluster(self) -> SpectrumCluster: - cluster = SpectrumCluster() - attr_set = self.cluster_attribute_sets.get('all') - if attr_set: - attr_set.apply(cluster) - return cluster - - def _analyte_interpretation_link(self, spectrum: Spectrum, - interpretation: Interpretation): - if (interpretation.has_attribute(ANALYTE_MIXTURE_TERM) and - not interpretation.analytes): - analyte_ids = interpretation.get_attribute(ANALYTE_MIXTURE_TERM) - if isinstance(analyte_ids, str): - term = self.find_term_for(ANALYTE_MIXTURE_CURIE) - analyte_ids = term.value_type(analyte_ids) - - # TODO: Enforce this attribute is a string at the CV level - # if isinstance(analyte_ids_term, int): - # analyte_ids = [analyte_ids_term] - # interpretation.replace_attribute(ANALYTE_MIXTURE_TERM, str(analyte_ids_term)) - # else: - # analyte_ids = analyte_ids_term.split(',') - for analyte_id in analyte_ids: - interpretation.add_analyte(spectrum.get_analyte(analyte_id)) - return interpretation - - def _default_interpretation_to_analytes(self, spectrum: Spectrum): - for interpretation in spectrum.interpretations.values(): - if not interpretation.analytes: - for analyte in spectrum.analytes.values(): - interpretation.add_analyte(analyte) - - def get_spectrum(self, spectrum_number: int=None, - spectrum_name: str=None) -> Spectrum: - """ - Retrieve a single spectrum from the library. - - Parameters - ---------- - spectrum_number : int, optional - The index of the spectrum in the library - spectrum_name : str, optional - The name of the spectrum in the library - - Returns - ------- - :class:`~.Spectrum` - """ - raise NotImplementedError() - - def get_cluster(self, cluster_number: int) -> SpectrumCluster: - """ - Retrieve a single spectrum cluster from the library. - - Parameters - ---------- - cluster_number : int, optional - The index of the cluster in the library - - Returns - ------- - :class:`~.SpectrumCluster` - """ - raise NotImplementedError() - - def find_spectra(self, specification, **query_keys): - raise NotImplementedError() - - def create_index(self) -> int: - """ - Populate the spectrum index. - - This method may produce a large amount of file I/O. - - Returns - ------- - n_spectra: int - The number of entries read - """ - raise NotImplementedError() - - def __iter__(self): - if self.index: - for record in self.index: - yield self.get_spectrum(record.number) - else: - return self.read() - - def __len__(self): - return len(self.index) - - def __getitem__(self, i) -> Union[Spectrum, List[Spectrum]]: - record = self.index[i] - if isinstance(record, list): - result = [self.get_spectrum(rec.number) for rec in record] - else: - result = self.get_spectrum(record.number) - return result - - @classmethod - def has_index_preference(cls, filename: Union[str, Path, io.FileIO]) -> Type[IndexBase]: - """ - Check if this backend prefers a particular index for this file. - - The base implementation checks to see if there is a SQL index - for the filename provided, and if so, prefers :class:`~.SQLIndex`. - Otherwise, prefers :class:`~.MemoryIndex`. - - Parameters - ---------- - filename: str - The name of the file to open. - - Returns - ------- - index_type: type - Returns a :class:`~.IndexBase` derived type which this backend - would prefer to use. - """ - try: - if SQLIndex.exists(filename): - return SQLIndex - return MemoryIndex - except Exception: - return MemoryIndex - - def read(self) -> Iterator[Union[Spectrum, SpectrumCluster]]: - """ - Create an sequential iterator over the spectrum library. - - Yields - ------ - entry : Union[:class:`~.Spectrum`, :class:`~.SpectrumCluster`] - """ - raise NotImplementedError() - - def _add_attribute_set(self, attribute_set: AttributeSet, - attribute_set_type: AttributeSetTypes): - if attribute_set_type == AttributeSetTypes.spectrum: - self.spectrum_attribute_sets[attribute_set.name] = attribute_set - elif attribute_set_type == AttributeSetTypes.analyte: - self.analyte_attribute_sets[attribute_set.name] = attribute_set - elif attribute_set_type == AttributeSetTypes.interpretation: - self.interpretation_attribute_sets[attribute_set.name] = attribute_set - elif attribute_set_type == AttributeSetTypes.cluster: - self.cluster_attribute_sets[attribute_set.name] = attribute_set - else: - raise ValueError(f"Could not map {attribute_set_type}") - - def summarize_parsing_errors(self) -> Dict: - return {} - - -guess_implementation = SpectralLibraryBackendBase.guess_implementation - - -class _PlainTextSpectralLibraryBackendBase(SpectralLibraryBackendBase): - - def __init__(self, filename: Union[str, Path, io.FileIO], index_type=None, - read_metadata: bool=True, create_index: bool=True): - if index_type is None and create_index: - index_type = self.has_index_preference(filename) - - super(_PlainTextSpectralLibraryBackendBase, self).__init__(filename) - - if index_type is not None: - self.index, was_initialized = index_type.from_filename(filename) - if not was_initialized and create_index: - self.create_index() - if read_metadata: - self.read_header() - - def _coerce_handle(self, filename_or_stream): - if hasattr(filename_or_stream, 'read'): - self.handle = filename_or_stream - else: - self.handle = open_stream(filename_or_stream, 'rt') - - def _buffer_from_stream(self, stream: io.IOBase) -> List: - """ - Collect data from the readable stream until - a complete spectrum entry has been observed. - - Parameters - ---------- - stream: file-like - Theinput file stream to read from. - - Returns - ------- - line_buffer: List[str] - A list of lines read from the input stream. - """ - raise NotImplementedError() - - def read(self) -> Iterator[Spectrum]: - with open_stream(self.filename, 'rb') as stream: - i = 0 - match, offset = self._parse_header_from_stream(stream) - if not match: - raise ValueError("Could not locate valid header") - else: - stream.seek(offset) - buffering_stream = _LineBuffer(stream, encoding="utf8") - while True: - # Will clip the first line of the next spectrum. Needs work - buffer = self._buffer_from_stream(buffering_stream) - - # If the buffer is only a single line, then we must have reached - # the end, so we're done. We're done because the buffering stream - # will contain exactly one line (the buffered line) - if len(buffer) <= 1: - break - buffering_stream.push_line() - yield self._parse(buffer, i) - i += 1 - - def _get_lines_for(self, offset: int) -> List[str]: - filename = self.filename - is_file_like_object = isinstance(filename, io.IOBase) - - infile = open_stream(filename, 'r') - - infile.seek(offset) - spectrum_buffer = self._buffer_from_stream(infile) - #### We will end up here if this is the last spectrum in the file - if not is_file_like_object: - infile.close() - else: - infile.detach() - return spectrum_buffer - - def _parse(self, buffer: Iterable, spectrum_index: int=None): - raise NotImplementedError() - - def search(self, specification, **query_keys) -> List[Spectrum]: - records = self.index.search(specification, **query_keys) - if not isinstance(records, list): - records = [records] - spectra = [] - for record in records: - buffer = self._get_lines_for(record.offset) - spectrum = self._parse(buffer, record.number) - spectra.append(spectrum) - return spectra - - -class _CSVSpectralLibraryBackendBase(SpectralLibraryBackendBase): - _delimiter: str - _header: List[str] - - _required_columns: List[str] = None - - @classmethod - def guess_from_header(cls, filename) -> bool: - with open_stream(filename, 'rt') as fh: - line = fh.readline() - tokens = line.split('\t') - if len(tokens) > 3: - warnings.warn( - "This file looks like a TSV file, but it's not possible to say definitively what" - " type from this alone. Please explicitly specify the format.") - return False - return False - - def __init__(self, filename: Union[str, Path, io.FileIO], index_type=None, delimiter='\t', - read_metadata: bool=True, create_index: bool = True, ** kwargs): - if index_type is None: - index_type = self.has_index_preference(filename) - self._delimiter = delimiter - self._headers = None - super().__init__(filename) - self.filename = filename - - self.read_header() - self.index, was_initialized = index_type.from_filename(filename) - if not was_initialized and create_index: - self.create_index() - - def read_header(self) -> bool: - self._read_header_line() - return True - - def _read_header_line(self): - headers = None - with open_stream(self.filename) as stream: - reader = csv.reader(stream, delimiter=self._delimiter) - headers = next(reader) - stream.seek(0) - self._headers = headers - if headers and self._required_columns: - missing_required = set(self._required_columns) - set(headers) - if missing_required: - raise TypeError( - f"{self.format_name} requires column{'s' if len(missing_required) > 1 else ''} " - f"{', '.join(missing_required)}, but were not found." - ) - - def _open_reader(self, stream: io.TextIOBase) -> Union[Iterator[Dict[str, Any]], csv.DictReader]: - return csv.DictReader(stream, fieldnames=self._headers, delimiter='\t') - - def get_spectrum(self, spectrum_number: int = None, spectrum_name: str = None) -> Spectrum: - # keep the two branches separate for the possibility that this is not possible with all - # index schemes. - if spectrum_number is not None: - if spectrum_name is not None: - raise ValueError("Provide only one of spectrum_number or spectrum_name") - offset = self.index.offset_for(spectrum_number) - elif spectrum_name is not None: - offset = self.index.offset_for(spectrum_name) - else: - raise ValueError("Must provide either spectrum_number or spectrum_name argument") - buffer = self._get_lines_for(offset) - spectrum = self._parse_from_buffer(buffer, spectrum_number) - return spectrum - - def _batch_rows(self, iterator: Iterator[Dict[str, Any]]) -> Iterator[List[Dict[str, Any]]]: - """ - Gather successive rows by some shared key into a batch to be parsed into a single - :class:`~.Spectrum` instance. - - This assumes there are no interleaved rows across spectra. - - Parameters - ---------- - iterator : Iterator[Dict[str, Any]] - An iterator over rows of the underlying CSV as dictionaries - - Yields - ------ - batch : List[Dict[str, Any]] - The next batch of rows corresponding to a single spectrum - """ - raise NotImplementedError() - - def _get_lines_for(self, offset: int) -> List[Dict[str, Any]]: - with open_stream(self.filename, 'r') as infile: - infile.seek(offset) - reader = self._open_reader(infile) - spectrum_buffer = next(self._batch_rows(reader)) - #### We will end up here if this is the last spectrum in the file - return spectrum_buffer - - def read(self) -> Iterator[Spectrum]: - with open_stream(self.filename, 'rt') as stream: - i = 0 - reader = self._open_reader(stream) - if self._headers: - # Skip the header line if we've already parsed them - _ = next(reader) - buffering_reader = self._batch_rows(reader) - for i, buffer in enumerate(buffering_reader): - yield self._parse_from_buffer(buffer, i) - - -class SpectralLibraryWriterBase(_VocabularyResolverMixin, metaclass=SubclassRegisteringMetaclass): - - def __init__(self, filename, **kwargs): - self.filename = filename - super().__init__(**kwargs) - - def _filter_attributes(self, attributes: Attributed, - filter_fn: Callable) -> Iterable: - if isinstance(attributes, AttributedEntity): - attributes = attributes.attributes - for attrib in attributes: - if filter_fn(attrib): - yield attrib - - def _not_analyte_mixture_term(self, attrib): - if attrib: - key = attrib[0] - if key == ANALYTE_MIXTURE_TERM: - return False - return True - - def _not_entry_index(self, attrib): - if attrib: - key = attrib[0] - if key == LIBRARY_SPECTRUM_INDEX: - return False - return True - - def _not_entry_key_or_index(self, attrib): - if attrib: - key = attrib[0] - if key in (LIBRARY_SPECTRUM_INDEX, LIBRARY_SPECTRUM_KEY): - return False - return True - - def _coerce_handle(self, filename_or_stream): - if hasattr(filename_or_stream, 'write'): - self.handle = filename_or_stream - else: - self.handle = open(filename_or_stream, 'wt') - - def write_library(self, library: SpectralLibraryBackendBase): - self.write_header(library) - n = len(library) - step = max(min(n // 100, 5000), 1) - ident = '' - i = 0 - for i, entry in enumerate(library.read()): - if i % step == 0 and i: - if isinstance(entry, SpectrumCluster): - tag = "cluster " - else: - tag = "" - try: - ident = f"{tag}{entry.key}:{entry.name}" - except Exception: - ident = f"{tag}{entry.key}" - logger.info(f"Wrote {ident} {i}/{n} ({i / n * 100.0:0.2f}%)") - if isinstance(entry, Spectrum): - self.write_spectrum(entry) - elif isinstance(entry, SpectrumCluster): - self.write_cluster(entry) - else: - raise TypeError(f"Don't know how to save {entry.__class__}") - - i = n - logger.info(f"Wrote {n} spectra") - - def write_spectrum(self, spectrum: Spectrum): - raise NotImplementedError() - - def write_cluster(self, cluster: SpectrumCluster): - raise NotImplementedError() - - def __enter__(self) -> 'SpectralLibraryWriterBase': - return self - - def __exit__(self, exc_type, exc_value, traceback): - self.close() - - def close(self): - pass - - -class LibraryIterator(AttributedEntity, _LibraryViewMixin, Iterator[Spectrum]): - """An iterator wrapper for a library source that doesn't permit random access""" - - backend: SpectralLibraryBackendBase - attributes: Attributed - iter: Iterator[Spectrum] - _buffer: Spectrum - - def __init__(self, backend: SpectralLibraryBackendBase) -> None: - self.backend = backend - self.attributes = backend - self.iter = backend.read() - self._buffer = next(self.iter) - - def __iter__(self): - return self - - def __next__(self) -> Spectrum: - if self._buffer is not None: - result = self._buffer - self._buffer = None - return result - return next(self.iter) diff --git a/implementations/python/mzlib/backends/bibliospec.py b/implementations/python/mzlib/backends/bibliospec.py deleted file mode 100644 index 78b1f10..0000000 --- a/implementations/python/mzlib/backends/bibliospec.py +++ /dev/null @@ -1,208 +0,0 @@ -import sqlite3 -import zlib -from dataclasses import dataclass - -from typing import Iterator, List, Mapping, Tuple, Iterable, Type - -import numpy as np - -from pyteomics import proforma - -from mzlib import annotation -from mzlib.analyte import FIRST_ANALYTE_KEY, FIRST_INTERPRETATION_KEY, Analyte -from mzlib.spectrum import Spectrum, SPECTRUM_NAME, CHARGE_STATE -from mzlib.attributes import AttributeManager, Attributed - -from mzlib.backends.base import SpectralLibraryBackendBase, FORMAT_VERSION_TERM, DEFAULT_VERSION - -from mzlib.index.base import IndexBase - - -class BibliospecBase: - connection: sqlite3.Connection - - def _correct_modifications_in_sequence(self, row: Mapping) -> proforma.ProForma: - """ - Correct the modifications in Bibliospec's modified peptide sequence. - - Bibliospec only stores modifications as delta masses. - """ - mods = self.connection.execute("SELECT * FROM Modifications WHERE RefSpectraID = ?", (row['id'], )).fetchall() - peptide = proforma.ProForma.parse(row["peptideModSeq"]) - for mod in mods: - position = mod['position'] - 1 - mass = mod['mass'] - peptide[position][1][0] = proforma.MassModification(mass) - return peptide - - - - -@dataclass -class BlibIndexRecord: - number: int - precursor_mz: float - precursor_charge: int - peptide: str - - -class BlibIndex(BibliospecBase, IndexBase): - connection: sqlite3.Connection - - def __init__(self, connection): - self.connection = connection - - def __getitem__(self, i): - if isinstance(i, int): - return self.search(i + 1) - elif isinstance(i, slice): - return [self.search(j + 1) for j in range(i.start or 0, i.stop or len(self), i.step or 1)] - else: - raise TypeError(f"Cannot index {self.__class__.__name__} with {i}") - - def _record_from(self, row: Mapping) -> BlibIndexRecord: - peptide_sequence = str(self._correct_modifications_in_sequence(row)) - return BlibIndexRecord(row['id'], row['precursorMZ'], row['precursorCharge'], peptide_sequence) - - def search(self, i): - if isinstance(i, int): - info = self.connection.execute("SELECT * FROM RefSpectra WHERE id = ?", (i, )).fetchone() - return self._record_from(info) - elif isinstance(i, str): - raise NotImplementedError() - - def __iter__(self): - return map(self._record_from, self.connection.execute("SELECT * FROM RefSpectra ORDER BY id").fetchall()) - - def __len__(self): - return self.connection.execute("SELECT count(*) FROM RefSpectra;").fetchone()[0] - - -class BibliospecSpectralLibrary(BibliospecBase, SpectralLibraryBackendBase): - """Read Bibliospec 2 SQLite3 spectral library files.""" - - connection: sqlite3.Connection - - file_format = "blib" - format_name = "bibliospec" - - @classmethod - def has_index_preference(cls, filename) -> Type[IndexBase]: - return BlibIndex - - def __init__(self, filename, **kwargs): - super().__init__(filename) - self.connection = sqlite3.connect(filename) - self.connection.row_factory = sqlite3.Row - self.index = BlibIndex(self.connection) - self.read_header() - - def read_header(self) -> bool: - attribs = AttributeManager() - attribs.add_attribute(FORMAT_VERSION_TERM, DEFAULT_VERSION) - attribs.add_attribute("MS:1003207|library creation software", "Bibliospec") - - info = self.connection.execute("SELECT * FROM LibInfo;").fetchone() - library_id = info['libLSID'] - _, pfx_name = library_id.split("bibliospec:") - _, name = pfx_name.split(":", 1) - attribs.add_attribute("MS:1003188|library name", name) - attribs.add_attribute("MS:1003187|library identifier", library_id) - attribs.add_attribute("MS:1003200|software version", f"{info['majorVersion']}.{info['minorVersion']}") - self.attributes = attribs - return True - - def _populate_analyte(self, analyte: Analyte, row: Mapping): - """ - Fill an analyte with details describing a peptide sequence and inferring - from context its traits based upon the assumptions Bibliospec makes. - - Bibliospec only stores modifications as delta masses. - """ - peptide = self._correct_modifications_in_sequence(row) - analyte.add_attribute("MS:1003169|proforma peptidoform sequence", str(peptide)) - analyte.add_attribute("MS:1001117|theoretical mass", peptide.mass) - analyte.add_attribute("MS:1000888|stripped peptide sequence", row['peptideSeq']) - analyte.add_attribute(CHARGE_STATE, row['precursorCharge']) - - def get_spectrum(self, spectrum_number: int = None, spectrum_name: str = None): - """ - Read a spectrum from the spectrum library. - - Bibliospec does not support alternative labeling of spectra with a - plain text name so looking up by `spectrum_name` is not supported. - """ - if spectrum_number is None: - raise ValueError("Only spectrum number queries are supported. spectrum_number must have an integer value") - try: - spectrum_number = int(spectrum_number) - except (ValueError, TypeError): - raise ValueError(f"spectrum_number must have an integer value, received {spectrum_number!r}") from None - info = self.connection.execute("SELECT * FROM RefSpectra WHERE id = ?", (spectrum_number, )).fetchone() - spectrum = self._new_spectrum() - spectrum.key = info['id'] - spectrum.index = info['id'] - 1 - spectrum.precursor_mz = info['precursorMZ'] - spectrum.add_attribute(CHARGE_STATE, info['precursorCharge']) - try: - spectrum.add_attribute("MS:1000894|retention time", info['retentionTime']) - except KeyError: - pass - - try: - spectrum.add_attribute("MS:1003069|number of replicate spectra available", info['copies']) - spectrum.add_attribute("MS:1003070|number of replicate spectra used", 1) - except KeyError: - pass - - n_peaks = info['numPeaks'] - spectrum.add_attribute("MS:1003059|number of peaks", n_peaks) - - try: - spectrum.add_attribute( - "MS:1003203|constituent spectrum file", - self.connection.execute("SELECT fileName FROM SpectrumSourceFiles WHERE id = ?", - (info['fileID'], )).fetchone()['fileName'] - ) - except KeyError: - pass - spectrum.add_attribute( - "MS:1003057|scan number", - info["SpecIDinFile"] - ) - - analyte = self._new_analyte(1) - self._populate_analyte(analyte, info) - - spectrum.add_analyte(analyte) - - interp = self._new_interpretation(1) - interp.add_analyte(analyte) - spectrum.add_interpretation(interp) - - peak_data = self.connection.execute("SELECT * FROM RefSpectraPeaks WHERE RefSpectraID = ?", (spectrum_number, )).fetchone() - try: - mz_array = np.frombuffer(zlib.decompress(peak_data['peakMZ']), dtype=np.float64) - except zlib.error: - mz_array = np.frombuffer(peak_data['peakMZ'], dtype=np.float64) - if mz_array.size != n_peaks: - raise ValueError(f"m/z array does not match expected peak count ({mz_array.size} != {n_peaks})") - - try: - intensity_array = np.frombuffer(zlib.decompress(peak_data['peakIntensity']), dtype=np.float32) - except zlib.error: - intensity_array = np.frombuffer(peak_data['peakIntensity'], dtype=np.float32) - if intensity_array.size != n_peaks: - raise ValueError(f"m/z array does not match expected peak count ({intensity_array.size} != {n_peaks})") - - peak_list = [] - for i, mz in enumerate(mz_array): - row = (mz, intensity_array[i], [], '') - peak_list.append(row) - spectrum.peak_list = peak_list - return spectrum - - def read(self) -> Iterator[Spectrum]: - for rec in self.index: - yield self.get_spectrum(rec.number) - diff --git a/implementations/python/mzlib/backends/diann.py b/implementations/python/mzlib/backends/diann.py deleted file mode 100644 index 1854485..0000000 --- a/implementations/python/mzlib/backends/diann.py +++ /dev/null @@ -1,239 +0,0 @@ -import json -import os - -from typing import List, Tuple, Dict, Iterator, Any, Union - -from pyteomics import proforma - -from mzlib import annotation -from mzlib.backends.base import DEFAULT_VERSION, FORMAT_VERSION_TERM, LIBRARY_NAME_TERM, _CSVSpectralLibraryBackendBase -from mzlib.backends.utils import open_stream, urlify -from mzlib.spectrum import Spectrum, SPECTRUM_NAME - - -def _rewrite_unimod_peptide_as_proforma(sequence: str) -> str: - return sequence.replace("(", '[').replace(')', ']').replace("UniMod", "UNIMOD") - - -CHARGE_STATE = "MS:1000041|charge state" -SELECTED_ION_MZ = "MS:1003053|theoretical monoisotopic m/z" -SOURCE_FILE = "MS:1003203|constituent spectrum file" -STRIPPED_PEPTIDE_TERM = "MS:1000888|stripped peptide sequence" -PROFORMA_PEPTIDE_TERM = "MS:1003169|proforma peptidoform sequence" - -CUSTOM_ATTRIBUTE_NAME = "MS:1003275|other attribute name" -CUSTOM_ATTRIBUTE_VALUE = "MS:1003276|other attribute value" - -NO_LOSS = 'noloss' - - -def _parse_value(value: str) -> Union[float, int, str, bool]: - try: - return json.loads(value) - except json.JSONDecodeError: - lower = value.lower() - if lower == "true": - return True - elif lower == "false": - return False - return value - - -class DIANNTSVSpectralLibrary(_CSVSpectralLibraryBackendBase): - format_name = "dia-nn.tsv" - - _custom_spectrum_keys = [ - "ExcludeFromAssay", - "AllowForNormalization", - ] - - _custom_analyte_keys = [ - "Proteotypic", - "ProteinGroup", - ] - - _required_columns = ['transition_group_id', 'PrecursorMz', 'PrecursorCharge', - 'FullUniModPeptideName', 'ProductMz', 'LibraryIntensity', - 'FragmentType', 'FragmentSeriesNumber', - 'FragmentCharge', 'FragmentLossType'] - - def __init__(self, filename: str, index_type=None, **kwargs): - super().__init__(filename, index_type=index_type, delimiter='\t', **kwargs) - - def _spectrum_type(self): - key = "MS:1003072|spectrum origin type" - value = "MS:1003074|predicted spectrum" - return key, value - - def read_header(self) -> bool: - result = super().read_header() - self.add_attribute(FORMAT_VERSION_TERM, DEFAULT_VERSION) - if hasattr(self.filename, 'name'): - name = self.filename.name.replace(".gz", '').rsplit('.', 1)[0].split(os.sep)[-1] - else: - name = self.filename.replace(".gz", '').rsplit(".", 1)[0].split(os.sep)[-1] - self.add_attribute(LIBRARY_NAME_TERM, name) - self.add_attribute("MS:1003207|library creation software", "MS:1003253|DIA-NN") - return result - - def create_index(self): - with open_stream(self.filename, 'rb') as stream: - header = stream.readline() - header_cols = header.split(b'\t') - column_key = header_cols.index(b'transition_group_id') - offset = stream.tell() - - line = stream.readline() - tokens = line.split(b'\t') - key = tokens[column_key] - index = {key: offset} - n = 0 - self.index.add( - number=n, - offset=offset, - name=key.decode("utf8"), - analyte=None - ) - n += 1 - - # To hold previous values - last_offset = None - last_key = None - while line: - tokens = line.split(b'\t') - if tokens[column_key] != key: - key = tokens[column_key] - self.index.add( - number=n, - offset=offset, - name=key.decode("utf8") , - analyte=None - ) - n += 1 - last_offset = stream.tell() - else: - offset = stream.tell() - line = stream.readline() - # self.index.add( - # number=n, - # offset=last_offset, - # name=tokens[column_key].decode('utf8'), - # analyte=None - # ) - n += 1 - self.index.commit() - return n - - def _parse_from_buffer(self, buffer: List[Dict[str, Any]], spectrum_index: int = None) -> Spectrum: - spec = self._new_spectrum() - descr = buffer[0] - - spec.add_attribute(SPECTRUM_NAME, descr['transition_group_id']) - spec.add_attribute(SELECTED_ION_MZ, float(descr['PrecursorMz'])) - - if 'FileName' in descr: - spec.add_attribute(SOURCE_FILE, urlify(descr['FileName'])) - spec.add_attribute(*self._spectrum_type()) - - if 'decoy' in descr and int(descr['decoy']): - spec.add_attribute("MS:1003072|spectrum origin type", "MS:1003192|decoy spectrum") - - if 'IonMobility' in descr: - spec.add_attribute("MS:1002476|ion mobility drift time", float(descr['IonMobility'])) - - analyte = self._new_analyte('1') - - pf_seq = _rewrite_unimod_peptide_as_proforma(descr['FullUniModPeptideName']) - peptide = proforma.ProForma.parse(pf_seq) - - if 'PeptideSequence' in descr: - analyte.add_attribute(STRIPPED_PEPTIDE_TERM, descr['PeptideSequence']) - analyte.add_attribute(PROFORMA_PEPTIDE_TERM, pf_seq) - analyte.add_attribute("MS:1001117|theoretical mass", peptide.mass) - analyte.add_attribute(CHARGE_STATE, int(descr['PrecursorCharge'])) - - protein_group_id = analyte.get_next_group_identifier() - if "UniprotID" in descr: - analyte.add_attribute( - "MS:1000885|protein accession", - descr['UniprotID'], - group_identifier=protein_group_id - ) - if "ProteinName" in descr: - analyte.add_attribute( - "MS:1000886|protein name", - descr["ProteinName"], - group_identifier=protein_group_id - ) - - for key in self._custom_analyte_keys: - if key in descr: - analyte.add_attribute_group([ - [CUSTOM_ATTRIBUTE_NAME, key], - [CUSTOM_ATTRIBUTE_VALUE, _parse_value(descr[key])] - ]) - - spec.add_analyte(analyte) - spec.peak_list = self._generate_peaks(buffer) - spec.add_attribute("MS:1003059|number of peaks", len(spec.peak_list)) - - for key in self._custom_spectrum_keys: - if key in descr: - spec.add_attribute_group([ - [CUSTOM_ATTRIBUTE_NAME, key], - [CUSTOM_ATTRIBUTE_VALUE, _parse_value(descr[key])] - ]) - - if spectrum_index is not None: - spec.index = spectrum_index - else: - spec.index = -1 - spec.key = spec.index + 1 - return spec - - def _generate_peaks(self, batch: List[Dict[str, Any]]) -> List[Tuple[float, float, List[annotation.IonAnnotationBase], List]]: - peaks = [] - for row in batch: - mz = float(row['ProductMz']) - intensity = float(row['LibraryIntensity']) - - series = row['FragmentType'] - ordinal = int(row['FragmentSeriesNumber']) - charge = int(row['FragmentCharge']) - - loss_type = row['FragmentLossType'] - if loss_type != NO_LOSS: - loss_type = ['-' + loss_type] - else: - loss_type = None - - annot = annotation.PeptideFragmentIonAnnotation( - series, ordinal, neutral_losses=loss_type, charge=charge, - mass_error=annotation.MassError(0, 'Da') - ) - - peak = [ - mz, intensity, [annot], [] - ] - peaks.append(peak) - return peaks - - def _batch_rows(self, iterator: Iterator[Dict[str, Any]]) -> Iterator[List[Dict[str, Any]]]: - group_key = None - group = [] - for row in iterator: - key = row['transition_group_id'] - if group_key is None: - group_key = key - group.append(row) - elif group_key == key: - group.append(row) - else: - yield group - group = [row] - group_key = key - if group: - yield group - - -DiaNNTSVSpectralLibrary = DIANNTSVSpectralLibrary diff --git a/implementations/python/mzlib/backends/encyclopedia.py b/implementations/python/mzlib/backends/encyclopedia.py deleted file mode 100644 index 4cd7abb..0000000 --- a/implementations/python/mzlib/backends/encyclopedia.py +++ /dev/null @@ -1,183 +0,0 @@ -import sqlite3 -import zlib -from dataclasses import dataclass - -from typing import Any, Iterator, List, Mapping, Tuple, Iterable, Type - -import numpy as np - -from pyteomics import proforma - -from mzlib import annotation -from mzlib.analyte import FIRST_ANALYTE_KEY, FIRST_INTERPRETATION_KEY, Analyte, ProteinDescription -from mzlib.spectrum import Spectrum, SPECTRUM_NAME, CHARGE_STATE -from mzlib.attributes import AttributeManager, Attributed, Attribute - -from mzlib.backends.base import SpectralLibraryBackendBase, FORMAT_VERSION_TERM, DEFAULT_VERSION - -from mzlib.index.base import IndexBase - - -DECOY_SPECTRUM = "MS:1003192|decoy spectrum" -DECOY_PEPTIDE_SPECTRUM = "MS:1003195|unnatural peptidoform decoy spectrum" - - -def _decode_peaks(record: sqlite3.Row): - raw_data = zlib.decompress(record['MassArray']) - mass_array = np.frombuffer(raw_data, dtype='>d') - raw_data = zlib.decompress(record['IntensityArray']) - intensity_array = np.frombuffer(raw_data, dtype='>f') - return mass_array, intensity_array - - -@dataclass -class EncyclopediaIndexRecord: - number: int - precursor_mz: float - precursor_charge: int - peptide: str - - -class EncyclopediaIndex(IndexBase): - connection: sqlite3.Connection - - def __init__(self, connection): - self.connection = connection - - def __getitem__(self, i): - if isinstance(i, int): - return self.search(i + 1) - elif isinstance(i, slice): - return [self.search(j + 1) for j in range(i.start or 0, i.stop or len(self), i.step or 1)] - else: - raise TypeError(f"Cannot index {self.__class__.__name__} with {i}") - - def _record_from(self, row: Mapping) -> EncyclopediaIndexRecord: - peptide_sequence = row['PeptideModSeq'] - return EncyclopediaIndexRecord(row['rowid'], row['PrecursorMz'], row['PrecursorCharge'], peptide_sequence) - - def search(self, i): - if isinstance(i, int): - info = self.connection.execute("SELECT rowid, PrecursorMz, PrecursorCharge, PeptideModSeq FROM entries WHERE rowid = ?", (i, )).fetchone() - return self._record_from(info) - elif isinstance(i, str): - raise NotImplementedError() - - def __iter__(self): - return map(self._record_from, self.connection.execute("SELECT rowid, PrecursorMz, PrecursorCharge, PeptideModSeq FROM entries ORDER BY rowid").fetchall()) - - def __len__(self): - return self.connection.execute("SELECT count(rowid) FROM entries;").fetchone()[0] - - -class EncyclopediaSpectralLibrary(SpectralLibraryBackendBase): - """Read EncyclopeDIA SQLite3 spectral library files.""" - - connection: sqlite3.Connection - - file_format = "dlib" - format_name = "encyclopedia" - - @classmethod - def has_index_preference(cls, filename) -> Type[IndexBase]: - return EncyclopediaIndex - - def __init__(self, filename: str, **kwargs): - super().__init__(filename) - self.connection = sqlite3.connect(filename) - self.connection.row_factory = sqlite3.Row - self.index = EncyclopediaIndex(self.connection) - self.read_header() - - def read_header(self) -> bool: - attribs = AttributeManager() - attribs.add_attribute(FORMAT_VERSION_TERM, DEFAULT_VERSION) - attribs.add_attribute("MS:1003207|library creation software", "EncyclopeDIA") - self.attributes = attribs - return True - - def _populate_analyte(self, analyte: Analyte, row: Mapping[str, Any]): - """ - Fill an analyte with details describing a peptide sequence and inferring - from context its traits based upon the assumptions EncyclopeDIA makes. - - EncyclopeDIA only stores modifications as delta masses. - """ - peptide = proforma.ProForma.parse(row['PeptideModSeq']) - analyte.add_attribute("MS:1003169|proforma peptidoform sequence", str(peptide)) - analyte.add_attribute("MS:1001117|theoretical mass", peptide.mass) - analyte.add_attribute("MS:1000888|stripped peptide sequence", row['PeptideSeq']) - analyte.add_attribute(CHARGE_STATE, row['PrecursorCharge']) - - cursor = self.connection.execute( - "SELECT ProteinAccession, isDecoy FROM peptidetoprotein WHERE PeptideSeq = ?;", (row['PeptideSeq'], )) - - had_decoy = False - for protrow in cursor: - accession = protrow['ProteinAccession'] - is_decoy = bool(int(protrow['isDecoy'])) - had_decoy = had_decoy or is_decoy - analyte.add_attribute_group([ - Attribute('MS:1000885|protein accession', accession) - ]) - return had_decoy - - def get_spectrum(self, spectrum_number: int = None, spectrum_name: str = None): - """ - Read a spectrum from the spectrum library. - - EncyclopeDIA does not support alternative labeling of spectra with a - plain text name so looking up by `spectrum_name` is not supported. - """ - if spectrum_number is None: - raise ValueError("Only spectrum number queries are supported. spectrum_number must have an integer value") - try: - spectrum_number = int(spectrum_number) - except (TypeError, ValueError): - raise ValueError(f"spectrum_number must have an integer value, received {spectrum_number!r}") from None - - info = self.connection.execute("SELECT rowid, * FROM entries WHERE rowid = ?;", (spectrum_number, )).fetchone() - spectrum = self._new_spectrum() - spectrum.key = info['rowid'] - spectrum.index = info['rowid'] - 1 - spectrum.precursor_mz = info['PrecursorMz'] - try: - spectrum.add_attribute("MS:1000894|retention time", info['RTInSeconds'] / 60.0) - except KeyError: - pass - - try: - spectrum.add_attribute( - "MS:1003203|constituent spectrum file", - f"file://{info['SourceFile']}" - ) - except KeyError: - pass - - - analyte = self._new_analyte(1) - had_decoy = self._populate_analyte(analyte, info) - if had_decoy: - spectrum.add_attribute(DECOY_SPECTRUM, DECOY_PEPTIDE_SPECTRUM) - - spectrum.add_analyte(analyte) - - interp = self._new_interpretation(1) - interp.add_analyte(analyte) - spectrum.add_interpretation(interp) - - mz_array, intensity_array = _decode_peaks(info) - n_peaks = len(mz_array) - spectrum.add_attribute("MS:1003059|number of peaks", n_peaks) - - peak_list = [] - # EncyclopeDIA does not encode product ion identities - for i, mz in enumerate(mz_array): - row = (mz, intensity_array[i], [], []) - peak_list.append(row) - spectrum.peak_list = peak_list - return spectrum - - def read(self) -> Iterator[Spectrum]: - for rec in self.index: - yield self.get_spectrum(rec.number) diff --git a/implementations/python/mzlib/backends/json.py b/implementations/python/mzlib/backends/json.py deleted file mode 100644 index 22df2fa..0000000 --- a/implementations/python/mzlib/backends/json.py +++ /dev/null @@ -1,511 +0,0 @@ -import io -import json -import logging -import warnings - -from typing import Any, Iterable, List, Dict, Mapping, Union - -from pathlib import Path -from mzlib.cluster import SpectrumCluster - -from mzlib.index import MemoryIndex -from mzlib.attributes import AttributeManager, Attributed, AttributeSet -from mzlib.annotation import parse_annotation, IonAnnotationBase -from mzlib.analyte import Analyte, Interpretation, FIRST_INTERPRETATION_KEY -from mzlib.spectrum import Spectrum - -from .base import SpectralLibraryBackendBase, SpectralLibraryWriterBase, FORMAT_VERSION_TERM, AttributeSetTypes -from .utils import open_stream - - -logger = logging.getLogger(__name__) -logger.addHandler(logging.NullHandler()) - - -LIBRARY_METADATA_KEY = "attributes" -ELEMENT_ATTRIBUTES_KEY = "attributes" -SPECTRA_KEY = "spectra" -CLUSTERS_KEY = "clusters" -FORMAT_VERSION_KEY = "format_version" -ANALYTES_KEY = 'analytes' -INTERPRETATIONS_KEY = 'interpretations' -INTERPRETATION_MEMBERS_KEY = 'members' -ID_KEY = 'id' - -MZ_KEY = "mzs" -INTENSITY_KEY = "intensities" -AGGREGATIONS_KEY = "aggregations" -PEAK_ANNOTATIONS_KEY = 'peak_annotations' - -SPECTRUM_CLASSES = "spectrum_attribute_sets" -ANALYTE_CLASSES = "analyte_attribute_sets" -INTERPRETATION_CLASSES = "interpretation_attribute_sets" -CLUSTER_CLASSES = "cluster_attribute_sets" - -FORMAT_VERSION_ACC = FORMAT_VERSION_TERM.split("|")[0] - - -class JSONSpectralLibrary(SpectralLibraryBackendBase): - """ - A reader for the JSON serialization of the mzSpecLib spectral library foramt. - - .. note:: - - Unlike other formats readers, this type does not parse incrementally, it instead - parses the entire JSON document in-memory and stores the parsed object structure. - The JSON objects are then converted into :mod:`mzlib` types upon request. This is - because incremental JSON parsing is substantially more difficult to do in a byte - aware manner, not to mention slow, in Python. - - This may lead to large memory overhead when reading large libraries in JSON format. - """ - - file_format = ["mzlb.json", "mzlib.json"] - format_name = "json" - - def __init__(self, filename, index_type=None, read_metadata=True): - if index_type is None: - index_type = MemoryIndex - super(JSONSpectralLibrary, self).__init__(filename) - self.buffer = {} - self._load_buffer(self.filename) - self.attributes = AttributeManager() - self.index, was_initialized = index_type.from_filename(self.filename) - if not was_initialized: - self.create_index() - if read_metadata: - self.read_header() - - @classmethod - def guess_from_filename(cls, filename: Union[str, Path, io.FileIO, Mapping]) -> bool: - if isinstance(filename, Mapping): - return SPECTRA_KEY in filename and LIBRARY_METADATA_KEY in filename - return super(JSONSpectralLibrary, cls).guess_from_filename(filename) - - def _load_buffer(self, filename_or_stream: Union[str, Path, io.FileIO, Mapping]): - if isinstance(filename_or_stream, Mapping): - self.buffer = filename_or_stream - else: - if hasattr(filename_or_stream, 'read'): - self.handle = filename_or_stream - else: - self.handle = open_stream(filename_or_stream, 'rt') - self.buffer = json.load(self.handle) - self.handle.close() - - def _load_attribute_sets(self, attribute_sets: dict): - return { - k: self._fill_attributes(v, AttributeSet(k, [])) for k, v in attribute_sets.items() - } - - def read_header(self) -> bool: - if self.buffer: - self._fill_attributes(self.buffer.get(LIBRARY_METADATA_KEY), self.attributes) - self.analyte_attribute_sets.update(self._load_attribute_sets(self.buffer.get(ANALYTE_CLASSES, {}))) - self.spectrum_attribute_sets.update(self._load_attribute_sets(self.buffer.get(SPECTRUM_CLASSES, {}))) - self.interpretation_attribute_sets.update(self._load_attribute_sets(self.buffer.get(INTERPRETATION_CLASSES, {}))) - return True - return False - - def create_index(self): - for i, record in enumerate(self.buffer.get(SPECTRA_KEY, [])): - name = None - key = None - for attrib in record['attributes']: - if attrib["accession"] == "MS:1003061": - name = attrib['value'] - if name and key: - break - if attrib["accession"] == "MS:1003237": - key = attrib['value'] - if name and key: - break - else: - if not name and not key: - raise ValueError(f"Unidentified spectrum at index {i}") - self.index.add(key, i, name, None, None) - for i, record in enumerate(self.buffer.get(CLUSTERS_KEY, [])): - key = None - for attrib in record[ELEMENT_ATTRIBUTES_KEY]: - if attrib["accession"] == "MS:1003267": - key = attrib['value'] - break - else: - if not name and not key: - raise ValueError(f"Unidentified spectrum cluster at index {i}") - self.index.add_cluster(key, i, None) - - def get_spectrum(self, spectrum_number: int=None, spectrum_name: str=None) -> Spectrum: - """ - Retrieve a single spectrum from the library. - - Parameters - ---------- - spectrum_number : int, optional - The index of the spectrum in the library - spectrum_name : str, optional - The name of the spectrum in the library - - Returns - ------- - :class:`~.Spectrum` - """ - if spectrum_number is not None: - if spectrum_name is not None: - raise ValueError( - "Provide only one of spectrum_number or spectrum_name") - offset = self.index.offset_for(spectrum_number) - elif spectrum_name is not None: - offset = self.index.offset_for(spectrum_name) - else: - raise ValueError("Must provide either spectrum_number or spectrum_name argument") - data = self.buffer[SPECTRA_KEY][offset] - spectrum = self._make_spectrum_from_payload(data) - return spectrum - - def get_cluster(self, cluster_number: int) -> SpectrumCluster: - offset = self.index.offset_for_cluster(cluster_number) - data = self.buffer[CLUSTERS_KEY][offset] - cluster = self._make_cluster_from_payload(data) - return cluster - - def _fill_attributes(self, attributes: List[Dict[str, Any]], store: Attributed, - context_type: AttributeSetTypes=None) -> Attributed: - last_group_id = None - current_group_id = None - for attrib in attributes: - if attrib['accession'] == "MS:1003212": - if context_type == AttributeSetTypes.analyte: - self.analyte_attribute_sets[attrib['value']].apply(store) - elif context_type == AttributeSetTypes.spectrum: - self.spectrum_attribute_sets[attrib['value']].apply(store) - elif context_type == AttributeSetTypes.interpretation: - self.interpretation_attribute_sets[attrib['value']].apply(store) - elif context_type == AttributeSetTypes.cluster: - self.cluster_attribute_sets[attrib['value']].apply(store) - else: - raise ValueError(f"Could not infer which attribute set type to use for {context_type}") - else: - key = f'{attrib["accession"]}|{attrib["name"]}' - if "value_accession" in attrib: - value = f'{attrib["value_accession"]}|{attrib["value"]}' - else: - value = attrib['value'] - - group = attrib.get("cv_param_group") - if group is not None: - if group != last_group_id: - current_group_id = store.get_next_group_identifier() - last_group_id = group - group = current_group_id - else: - group = current_group_id - - store.add_attribute(key, value, group_identifier=group) - return store - - def _make_analyte_from_payload(self, analyte_id, analyte_d: Dict) -> Analyte: - if analyte_id != analyte_d.get('id'): - warnings.warn( - f"An analyte with explicit id {analyte_d['id']!r} does not match its key {analyte_id!r}") - analyte = self._new_analyte(analyte_id) - self._fill_attributes(analyte_d[ELEMENT_ATTRIBUTES_KEY], analyte, AttributeSetTypes.analyte) - return analyte - - def _make_interpretation_from_payload(self, interpretation_id, interpretation_d: Dict) -> Interpretation: - if interpretation_id != interpretation_d.get('id'): - warnings.warn( - f"An analyte with explicit id {interpretation_d['id']!r} does not match its key {interpretation_id!r}") - - interpretation = self._new_interpretation(interpretation_id) - self._fill_attributes( - interpretation_d[ELEMENT_ATTRIBUTES_KEY], - interpretation.attributes, AttributeSetTypes.interpretation) - if INTERPRETATION_MEMBERS_KEY in interpretation_d: - for member_id, member in interpretation_d[INTERPRETATION_MEMBERS_KEY].items(): - member_d = self._new_interpretation_member(member_id) - self._fill_attributes( - member[ELEMENT_ATTRIBUTES_KEY], - member_d) - interpretation.add_member_interpretation(member_d) - return interpretation - - def _make_cluster_from_payload(self, data: Dict[str, Any]) -> SpectrumCluster: - cluster = self._new_cluster() - self._fill_attributes( - data[ELEMENT_ATTRIBUTES_KEY], cluster, AttributeSetTypes.cluster) - return cluster - - def _make_spectrum_from_payload(self, data: Dict) -> Spectrum: - spectrum = self._new_spectrum() - self._fill_attributes( - data[ELEMENT_ATTRIBUTES_KEY], - spectrum, - AttributeSetTypes.spectrum - ) - if ANALYTES_KEY in data: - for analyte_id, analyte in data[ANALYTES_KEY].items(): - analyte_d = self._make_analyte_from_payload(analyte_id, analyte) - spectrum.add_analyte(analyte_d) - - if INTERPRETATIONS_KEY in data: - for interpretation_id, interpretation_d in data[INTERPRETATIONS_KEY].items(): - interpretation = self._make_interpretation_from_payload( - interpretation_id, - interpretation_d - ) - spectrum.add_interpretation(interpretation) - self._analyte_interpretation_link(spectrum, interpretation) - self._default_interpretation_to_analytes(spectrum) - - peak_list = [] - n = len(data[MZ_KEY]) - mzs = data[MZ_KEY] - intensities = data[INTENSITY_KEY] - interpretations = data[PEAK_ANNOTATIONS_KEY] - aggregations = data.get(AGGREGATIONS_KEY, None) - for i in range(n): - interpretation = interpretations[i] - if isinstance(interpretation, str): - interpretation = parse_annotation(interpretation) - elif isinstance(interpretation, list): - interpretation = [IonAnnotationBase.from_json(interp) for interp in interpretation] - elif isinstance(interpretation, dict): - interpretation = [IonAnnotationBase.from_json(interpretation)] - else: - raise TypeError(f"Cannot reconstruct interpretation from type {interpretation.__class__}") - peak = [ - mzs[i], - intensities[i], - parse_annotation(interpretations[i]), - aggregations[i] if aggregations else '' - ] - peak_list.append(peak) - spectrum.peak_list = peak_list - return spectrum - - def read(self): - n = len(self.buffer.get(CLUSTERS_KEY, [])) - for offset in range(n): - data = self.buffer[CLUSTERS_KEY][offset] - cluster = self._make_cluster_from_payload(data) - yield cluster - - n = len(self.buffer[SPECTRA_KEY]) - for offset in range(n): - data = self.buffer[SPECTRA_KEY][offset] - spectrum = self._make_spectrum_from_payload(data) - yield spectrum - - -class JSONSpectralLibraryWriter(SpectralLibraryWriterBase): - """ - Write a spectral library to the JSON serialization of the mzSpecLib spectral library foramt. - - .. note:: - - Unlike other format writers, this writer buffers the entire library in memory as JSON-compatible - Python objects until the entire library is ready to be written out. This is because incrementally - writing JSON is substantially more difficult to do correctly. - - This may lead to large memory overhead when writing large libraries in JSON format. - """ - - file_format = "mzlb.json" - format_name = "json" - default_version = '1.0' - - def __init__(self, filename, version=None, pretty_print=True, format_annotations=True, simplify=True, **kwargs): - if version is None: - version = self.default_version - super(JSONSpectralLibraryWriter, self).__init__(filename) - self._coerce_handle(self.filename) - self.version = version - self.pretty_print = pretty_print - self.wrote_library = False - self.simplify = simplify - self.format_annotations = format_annotations - self.buffer = { - FORMAT_VERSION_KEY: self.version, - LIBRARY_METADATA_KEY: [], - SPECTRA_KEY: [], - CLUSTERS_KEY: [], - SPECTRUM_CLASSES: {}, - ANALYTE_CLASSES: {}, - INTERPRETATION_CLASSES: {}, - } - - def write_library(self, library: SpectralLibraryBackendBase): - self.wrote_library = True - return super().write_library(library) - - def split_compound_value(self, value): - value = str(value) - # Don't process quoted values - if value.startswith('"'): - return [value] - components = value.split('|', 1) - return components - - def write_header(self, library: SpectralLibraryBackendBase): - attributes = self._format_attributes(library.attributes) - self.buffer[LIBRARY_METADATA_KEY] = attributes - self.buffer[SPECTRUM_CLASSES] = { - c.name: self._format_attributes(c.attributes) for c in library.spectrum_attribute_sets.values() - } - self.buffer[ANALYTE_CLASSES] = { - c.name: self._format_attributes(c.attributes) for c in library.analyte_attribute_sets.values() - } - self.buffer[INTERPRETATION_CLASSES] = { - c.name: self._format_attributes(c.attributes) for c in library.interpretation_attribute_sets.values() - } - - def _format_attributes(self, attributes_manager: Iterable) -> List: - attributes = [] - for attribute in attributes_manager: - reformed_attribute = {} - key = attribute.key - value = attribute.value - if attribute.group_id is not None: - cv_param_group = attribute.group_id - reformed_attribute['cv_param_group'] = cv_param_group - - term = None - components = key.split('|', 1) - if len(components) == 2: - accession, name = components - reformed_attribute['accession'] = accession - reformed_attribute['name'] = name - try: - term = self.find_term_for(accession) - except KeyError: - pass - else: - raise ValueError( - f"Unsupported number of items in components: {components}") - - components = self.split_compound_value(value) - if len(components) == 2: - value_accession, value = components - reformed_attribute['value_accession'] = value_accession - reformed_attribute['value'] = value - elif len(components) == 1: - # If an attribute could take on a JSON-incompatible type, we would need to - # cast it here. - reformed_attribute['value'] = value - else: - raise ValueError( - f"Unsupported number of items in components: {components}") - attributes.append(reformed_attribute) - return attributes - - def write_cluster(self, cluster: SpectrumCluster): - attributes = self._format_attributes( - cluster.attributes - ) - payload = { - ELEMENT_ATTRIBUTES_KEY: attributes - } - self.buffer[CLUSTERS_KEY].append(payload) - - def write_spectrum(self, spectrum: Spectrum): - mzs = [] - intensities = [] - annotations = [] - aggregations = [] - for peak in spectrum.peak_list: - mzs.append(peak[0]) - intensities.append(peak[1]) - if self.format_annotations: - annotations.append( - '?' if not peak[2] else ",".join(map(str, peak[2]))) - else: - annotations.append([c.to_json() for c in peak[2]]) - aggregations.append(peak[3]) - - #### Organize the attributes from the simple list into the appropriate JSON format - attributes = self._format_attributes( - list(self._filter_attributes( - spectrum.attributes, - self._not_entry_index) - ) - ) - - analytes = {} - for analyte in spectrum.analytes.values(): - analyte_d = { - ID_KEY: analyte.id, - ELEMENT_ATTRIBUTES_KEY: self._format_attributes(analyte) - } - analytes[analyte.id] = (analyte_d) - - interpretations = {} - for interpretation in spectrum.interpretations.values(): - if len(analytes) == 1: - attribs_of = self._filter_attributes(interpretation, self._not_analyte_mixture_term) - else: - attribs_of = interpretation.attributes - interpretation_d = { - ID_KEY: interpretation.id, - ELEMENT_ATTRIBUTES_KEY: self._format_attributes(attribs_of), - } - interpretations[interpretation.id] = interpretation_d - if interpretation.member_interpretations: - members_d = interpretation_d[INTERPRETATION_MEMBERS_KEY] = {} - for member in interpretation.member_interpretations.values(): - members_d[member.id] = { - ID_KEY: member.id, - ELEMENT_ATTRIBUTES_KEY: self._format_attributes(member) - } - - payload = { - ELEMENT_ATTRIBUTES_KEY: attributes, - MZ_KEY: mzs, - INTENSITY_KEY: intensities, - PEAK_ANNOTATIONS_KEY: annotations, - AGGREGATIONS_KEY: aggregations, - ANALYTES_KEY: analytes, - INTERPRETATIONS_KEY: interpretations - } - if not any(aggregations): - payload.pop(AGGREGATIONS_KEY) - - self.buffer[SPECTRA_KEY].append(payload) - - def flush(self): - # If we know we're writing a complete library, skip the probably-doing-too-many-things - # formatting logic for single vs. many spectra. - if self.wrote_library: - if self.pretty_print: - json.dump(self.buffer, self.handle, indent=2, sort_keys=True) - else: - json.dump(self.buffer, self.handle) - else: - # We don't have a header section to format, so write just the spectra, - # and if the number of spectra is one and the simplify flag is true, - # skip the wrapping array - spectra = self.buffer[SPECTRA_KEY] - n_spectra = len(spectra) - if n_spectra == 1 and self.simplify: - if self.pretty_print: - json.dump(spectra[0], self.handle, - indent=2, sort_keys=True) - else: - json.dump(spectra[0], self.handle) - else: - if self.pretty_print: - json.dump(spectra, self.handle, indent=2, sort_keys=True) - else: - json.dump(spectra, self.handle) - - def close(self): - self.flush() - self.handle.close() - - -def format_spectrum(spectrum: Spectrum, pretty_print=True, **kwargs) -> str: - buffer = io.StringIO() - with JSONSpectralLibraryWriter(buffer, pretty_print=pretty_print, **kwargs) as writer: - writer.write_spectrum(spectrum) - writer.flush() - return buffer.getvalue() diff --git a/implementations/python/mzlib/backends/msp.py b/implementations/python/mzlib/backends/msp.py deleted file mode 100644 index 68cbe00..0000000 --- a/implementations/python/mzlib/backends/msp.py +++ /dev/null @@ -1,1692 +0,0 @@ -import re -import io -import os -import logging -import itertools -import warnings - -from typing import ( - Any, Callable, Collection, - Dict, List, Mapping, Optional, - Set, Tuple, Iterable, DefaultDict) - -from pyteomics import proforma - -from mzlib import annotation - -from mzlib.analyte import FIRST_ANALYTE_KEY, FIRST_INTERPRETATION_KEY, Analyte, ProteinDescription -from mzlib.spectrum import Spectrum, SPECTRUM_NAME -from mzlib.attributes import AttributeManager, AttributeSet, Attributed - -from .base import ( - DEFAULT_VERSION, FORMAT_VERSION_TERM, _PlainTextSpectralLibraryBackendBase, - LIBRARY_NAME_TERM, AttributeSetTypes, SpectralLibraryBackendBase, - SpectralLibraryWriterBase) -from .utils import try_cast, open_stream, CaseInsensitiveDict - - -logger = logging.getLogger(__name__) -logger.addHandler(logging.NullHandler()) - -# TODO: Name: could be Compound or SpectrumName -leader_terms = { - "Name": SPECTRUM_NAME, - "NAME": SPECTRUM_NAME, - "Compound": SPECTRUM_NAME, - "COMPOUND": SPECTRUM_NAME, -} - - -def _generate_numpeaks_keys(): - w1 = "num" - w2 = "peaks" - seps = (" ", "") - cases = (str.lower, str.title, str.upper) - w1_cases = [c(w1) for c in cases] - w2_cases = [c(w2) for c in cases] - return {(w1c + sep + w2c) for (sep, w1c, w2c) in - itertools.product(seps, w1_cases, w2_cases)} - -NUM_PEAKS_KEYS = _generate_numpeaks_keys() - -leader_terms_pattern = re.compile(r"(Name|NAME|Compound|COMPOUND)\s*:") -leader_terms_line_pattern = re.compile(r'(?:Name|NAME|Compound|COMPOUND)\s*:\s+(.+)') - -STRIPPED_PEPTIDE_TERM = "MS:1000888|stripped peptide sequence" -PEPTIDE_MODIFICATION_TERM = "MS:1001471|peptide modification details" - -PEAK_OBSERVATION_FREQ = "MS:1003279|observation frequency of peak" -PEAK_ATTRIB = "MS:1003254|peak attribute" - - -class AttributeHandler: - keys: Collection[str] - - def __init__(self, keys: Collection[str]): - if isinstance(keys, str): - keys = (keys, ) - self.keys = keys - - def __contains__(self, key): - return key in self.keys - - def add_value(self, key: str, value: Any, container: Attributed): - container.add_attribute(key, value) - - def add_group(self, keys: List[str], values: List[Any], container: Attributed): - group_id = container.get_next_group_identifier() - for k, v in zip(keys, values): - container.add_attribute(k, v, group_id) - - def handle(self, key: str, value: Any, container: Attributed) -> bool: - raise NotImplementedError() - - def __call__(self, key: str, value: Any, container: Attributed) -> bool: - return self.handle(key, value, container) - - def chain(self, handler: 'AttributeHandler') -> 'AttributeHandlerChain': - return AttributeHandlerChain([self, handler]) - - def __and__(self, handler: 'AttributeHandler') -> 'AttributeHandlerChain': - return self.chain(handler) - - -class MappingAttributeHandler(AttributeHandler): - keys: Dict[str, Any] - - def __init__(self, keys: Dict[str, Any]): - self.keys = keys - - def handle(self, key: str, value: Any, container: Attributed) -> bool: - trans_key = self.keys[key] - if value is None: - if isinstance(trans_key, list): - k, v = trans_key - v = try_cast(v) - self.add_value(k, v, container) - else: - return False - elif isinstance(trans_key, str): - self.add_value(trans_key, try_cast(value), container) - elif isinstance(trans_key, dict): - if value in trans_key: - # If the mapping is a plain string, add it - if isinstance(trans_key[value], str): - key, value = trans_key[value].split("=") - self.add_value(key, try_cast(value), container) - # Or if it is a list, then there are multiple terms to add within a group - elif isinstance(trans_key[value], list): - if len(trans_key[value]) == 1: - for item in trans_key[value]: - self.add_value(item[0], try_cast(item[1]), container) - else: - k, v = zip(*trans_key[value]) - self.add_group(k, map(try_cast, v), container) - else: - return False - elif isinstance(trans_key, AttributeHandler): - return trans_key(key, value, container) - return True - - -class AttributeHandlerChain: - chain: List[AttributeHandler] - - def __init__(self, chain: List[AttributeHandler]): - self.chain = chain - - def handle(self, key: str, value: Any, container: Attributed) -> bool: - result = True - for handler in self.chain: - result |= handler.handle(key, value, container) - if not result: - return result - return result - - def __contains__(self, key): - for handler in self.chain: - if key in handler: - return True - return False - - def __iter__(self): - return iter(self.chain) - - def __call__(self, key: str, value: Any, container: Attributed) -> bool: - return self.handle(key, value, container) - - def chain(self, handler: 'AttributeHandler') -> 'AttributeHandlerChain': - return self.__class__(self.chain + [handler]) - - def add(self, handler: AttributeHandler): - self.chain.append(handler) - return handler - - -class RegexAttributeHandler(AttributeHandler): - pattern: re.Pattern - variable_attributes: List[str] - constant_attributes: Optional[List[Tuple[str, Any]]] - - def __init__(self, keys: Collection[str], pattern: re.Pattern, variable_attributes, constant_attributes=None): - super().__init__(keys) - self.pattern = pattern - self.variable_attributes = variable_attributes - self.constant_attributes = constant_attributes - - def handle(self, key: str, value: Any, container: Attributed) -> bool: - match = self.pattern.match(value) - if match: - if self.constant_attributes: - ks, vs = map(list, zip(*self.constant_attributes)) - ks.extend(self.variable_attributes) - vs.extend(match.groups()) - self.add_group(ks, vs, container) - else: - self.add_value(self.variable_attributes[0], match.group(1), container) - return True - return False - - -class FunctionAttributeHandler(AttributeHandler): - func: Callable[[str, Any, Attributed], bool] - - def __init__(self, keys: Collection[str], func: Callable[[str, Any, Attributed], bool]): - super().__init__(keys) - self.func = func - - def handle(self, key: str, value: Any, container: Attributed) -> bool: - return self.func(key, value, container) - - @classmethod - def wraps(cls, *keys): - def wrapper(func): - return cls(keys, func) - return wrapper - - -class DispatchingAttributeHandler(AttributeHandlerChain): - mapping: Dict[str, AttributeHandler] - - def __init__(self, chain: List[AttributeHandler] = None): - if not chain: - chain = [] - super().__init__(chain) - self.mapping = CaseInsensitiveDict() - for handler in self: - for key in handler.keys: - self.mapping[key] = handler - - def handle(self, key: str, value: Any, container: Attributed) -> bool: - handler = self.mapping[key] - return handler(key, value, container) - - def __contains__(self, key): - return key in self.mapping - - def add(self, handler: AttributeHandler): - super().add(handler) - for key in handler.keys: - self.mapping[key] = handler - return handler - - - -analyte_terms = CaseInsensitiveDict({ - "Charge": "MS:1000041|charge state", - "precursor_charge": "MS:1000041|charge state", - "precursorcharge": "MS:1000041|charge state", - - "MW": "MS:1000224|molecular mass", - "total exact mass": "MS:1000224|molecular mass", - "ExactMass": "MS:1000224|molecular mass", - "exact_mass": "MS:1000224|molecular mass", - "exact mass": "MS:1000224|molecular mass", - "molecular formula": "MS:1000866|molecular formula", - "Formula": "MS:1000866|molecular formula", - "formula": "MS:1000866|molecular formula", - "SMILES": "MS:1000868|SMILES formula", - "InChIKey": "MS:1002894|InChIKey", - # "Theo_mz_diff": "MS:1003209|monoisotopic m/z deviation", - "Scan": { - "Mods": PEPTIDE_MODIFICATION_TERM, - "Naa": "MS:1003043|number of residues", - }, - "Pep": { - "Tryptic": [["MS:1003048|number of enzymatic termini", 2], ["MS:1001045|cleavage agent name", "MS:1001251|Trypsin"]], - "SemiTryptic": [["MS:1003048|number of enzymatic termini", 1], ["MS:1001045|cleavage agent name", "MS:1001251|Trypsin"]], - "N-Semitryptic": [["MS:1003048|number of enzymatic termini", 1], ["MS:1001045|cleavage agent name", "MS:1001251|Trypsin"]], - "C-Semitryptic": [["MS:1003048|number of enzymatic termini", 1], ["MS:1001045|cleavage agent name", "MS:1001251|Trypsin"]], - "Tryptic/miss_good_confirmed": [["MS:1003048|number of enzymatic termini", 2], - ["MS:1003044|number of missed cleavages", "0"], - ["MS:1001045|cleavage agent name", "MS:1001251|Trypsin"]], - "Tryptic/miss_bad_confirmed": [["MS:1003048|number of enzymatic termini", 2], - ["MS:1003044|number of missed cleavages", ">0"], - ["MS:1001045|cleavage agent name", "MS:1001251|Trypsin"]], - }, - "MC": "MS:1003044|number of missed cleavages", - "Mods": PEPTIDE_MODIFICATION_TERM, - "Naa": "MS:1003043|number of residues", - "PrecursorMonoisoMZ": "MS:1003208|experimental precursor monoisotopic m/z", - "Mz_exact": "MS:1003208|experimental precursor monoisotopic m/z", - "Mz_av": "MS:1003054|theoretical average m/z", -}) - - -_HCD = ["MS:1000044|dissociation method", "MS:1000422|beam-type collision-induced dissociation"] - -# TODO: qtof -> CAD -instrument_dispatch = CaseInsensitiveDict({ - "it": [["MS:1000044|dissociation method", "MS:1002472|trap-type collision-induced dissociation"]], - "hcd": [_HCD], - "QExactive": [_HCD], - "Elite": [_HCD], -}) - - -other_terms = CaseInsensitiveDict({ - "Parent": "MS:1003208|experimental precursor monoisotopic m/z", - "ObservedPrecursorMZ": "MS:1003208|experimental precursor monoisotopic m/z", - "PrecursorMZ": "MS:1003208|experimental precursor monoisotopic m/z", - "PRECURSORMZ": "MS:1003208|experimental precursor monoisotopic m/z", - "precursor": "MS:1003208|experimental precursor monoisotopic m/z", - "precursor_mass": "MS:1003208|experimental precursor monoisotopic m/z", - "precursormass": "MS:1003208|experimental precursor monoisotopic m/z", - - "Single": ["MS:1003065|spectrum aggregation type", "MS:1003066|singleton spectrum"], - "Consensus": ["MS:1003065|spectrum aggregation type", "MS:1003067|consensus spectrum"], - "Inst": instrument_dispatch, - "Instrument_type": instrument_dispatch, - "Spec": {"Consensus": [["MS:1003065|spectrum aggregation type", "MS:1003067|consensus spectrum"]]}, - "Scan": "MS:1003057|scan number", - "Origfile": "MS:1003203|constituent spectrum file", - "filename": "MS:1003203|constituent spectrum file", - "file_name": "MS:1003203|constituent spectrum file", - "Sample": "MS:1000002|sample name", - "Filter": "MS:1000512|filter string", - "FTResolution": "MS:1000028|detector resolution", - "ms1PrecursorAb": "MS:1003085|previous MS1 scan precursor intensity", - "Precursor1MaxAb": "MS:1003086|precursor apex intensity", - "Purity": "MS:1009013|isolation window precursor purity", - "Num peaks": "MS:1003059|number of peaks", - "Num Peaks": "MS:1003059|number of peaks", - "num_peaks": "MS:1003059|number of peaks", - "numpeaks": "MS:1003059|number of peaks", - "Run": "MS:1003203|constituent spectrum file", - "Splash": "MS:1002599|splash key", -}) - - -@FunctionAttributeHandler.wraps("num_unassigned_peaks") -def unassigned_peaks_handler(key: str, value: str, container: Attributed) -> bool: - is_top_20 = False - if isinstance(value, str): - if "/" in value: - if "/20" in value: - is_top_20 = True - value = value.split("/")[0] - value = int(value) - if is_top_20: - container.add_attribute("MS:1003290|number of unassigned peaks among top 20 peaks", value) - else: - container.add_attribute("MS:1003288|number of unassigned peaks", value) - return True - - -interpretation_terms = CaseInsensitiveDict({ - "Unassigned_all_20ppm": "MS:1003079|total unassigned intensity fraction", - "Unassign_all": "MS:1003079|total unassigned intensity fraction", - - "top_20_num_unassigned_peaks_20ppm": "MS:1003290|number of unassigned peaks among top 20 peaks", - "num_unassigned_peaks_20ppm": unassigned_peaks_handler, - "num_unassigned_peaks": unassigned_peaks_handler, - - "max_unassigned_ab_20ppm": "MS:1003289|intensity of highest unassigned peak", - "max_unassigned_ab": "MS:1003289|intensity of highest unassigned peak", - - "Unassigned_20ppm": "MS:1003080|top 20 peak unassigned intensity fraction", - "Unassigned": "MS:1003080|top 20 peak unassigned intensity fraction", -}) - - -interpretation_member_terms = CaseInsensitiveDict({ - "Q-value": "MS:1002354|PSM-level q-value", -}) - - -species_map = { - "human": [["MS:1001467|taxonomy: NCBI TaxID", "NCBITaxon:9606|Homo sapiens"], - ["MS:1001469|taxonomy: scientific name", - "Homo sapiens"], - ["MS:1001468|taxonomy: common name", "human"]], - "zebrafish": [["MS:1001467|taxonomy: NCBI TaxID", "NCBITaxon:7955|Danio rerio"], - ["MS:1001469|taxonomy: scientific name", - "Danio rerio"], - ["MS:1001468|taxonomy: common name", "zebra fish"]], - "chicken": [["MS:1001467|taxonomy: NCBI TaxID", "NCBITaxon:9031|Gallus gallus"], - ["MS:1001469|taxonomy: scientific name", - "Gallus gallus"], - ["MS:1001468|taxonomy: common name", "chicken"]], - "rat": [ - ["MS:1001467|taxonomy: NCBI TaxID", "NCBITaxon:10116|Rattus norvegicus"], - ["MS:1001469|taxonomy: scientific name", - "Rattus norvegicus"], - ["MS:1001468|taxonomy: common name", "rat"] - ] -} - - -MODIFICATION_NAME_MAP = { - "CAM": "Carbamidomethyl", - "Pyro_glu": "Glu->pyro-Glu", # Resolves UNIMOD ambiguity - "Pyro-glu": "Gln->pyro-Glu", - "Oxidation": "Oxidation", - "Phospho": "Phospho", - "TMT6plex": "TMT6plex", - "iTRAQ": "iTRAQ", - "Acetyl": "Acetyl", - "TMT": "TMT6plex", -} - -TERMINAL_MODIFICATIONS = { - "Acetyl", - "TMT6plex" -} - - -# TODO: ppm is unsigned, add mass calculation to determine true mass accuracy - -annotation_pattern = re.compile(r"""^ -(?:(?:(?P[abyxcz]\.?)(?P\d+))| - (:?(?P(?:Int/[ARNDCEQGHKMFPSTWYVILJarndceqghkmfpstwyvilj]+)|(?:[mM](?P\d+):(?P\d+))))| - (?Pp)| - (:?I(?P[ARNDCEQGHKMFPSTWYVIL])(?:(?PCAM)|[A-Z])?)| - (?P(?PTMT|ITRAQ|iTRAQ)(?P\d+[NC]?))| - (?:_(?P[^\s,/]+))| - (?P\?) -) -(?P((?:[+-]\d*[A-Z][A-Za-z0-9]*)|(?:[+-]iTRAQ|TMT)|(?:[+-]\d+?(?!i)))+)? -(?:(?:\[M(?P(:?[+-]\d*[A-Z][A-Za-z0-9]*)+)\])? -(?:\^(?P[+-]?\d+))? -(?:(?P[+-]?\d*)i)?)+ -(?:/(?:Dev=)?(?P[+-]?\d+(?:\.\d+))(?Pppm)?)? -""", re.X) - - -class MSPAnnotationStringParser(annotation.AnnotationStringParser): - def _dispatch(self, annotation_string, data, adducts, charge, isotope, neutral_losses, analyte_reference, mass_error, confidence, **kwargs): - data['sequence_ordinal'] = None - data['sequence_internal'] = None - return super()._dispatch(annotation_string, data, adducts, charge, isotope, neutral_losses, analyte_reference, mass_error, confidence, **kwargs) - - def _dispatch_internal_peptide_fragment(self, data: Dict[str, Any], adducts: List, charge: int, isotope: int, neutral_losses: List, - analyte_reference: Any, mass_error: Any, **kwargs): - if data['internal_start']: - # The hybrid pattern detected an m: type string, not an Int/seq string - return super(MSPAnnotationStringParser, self)._dispatch_internal_peptide_fragment( - data, adducts, charge, isotope, neutral_losses, analyte_reference, mass_error, **kwargs) - - spectrum = kwargs.get("spectrum") - if spectrum is None: - raise ValueError("Cannot infer sequence coordinates from MSP internal fragmentation notation without" - " a reference to the spectrum, please pass spectrum as a keyword argument") - sequence = self._get_peptide_sequence_for_analyte( - spectrum, analyte_reference) - subseq = data['series_internal'] - if subseq.startswith("Int/"): - subseq = subseq[4:] - subseq = subseq.upper() - try: - start_index = sequence.index(subseq) - except ValueError as err: - raise ValueError( - f"Cannot locate internal subsequence {subseq} in {sequence}") from err - end_index = start_index + len(subseq) - data['internal_start'] = start_index + 1 - data['internal_end'] = end_index - return super(MSPAnnotationStringParser, self)._dispatch_internal_peptide_fragment( - data, adducts, charge, isotope, neutral_losses, analyte_reference, mass_error, **kwargs) - - def _coerce_isotope(self, data): - value = data.get('isotope') - if value is not None: - if value == '': - data['isotope'] = '1' - return super()._coerce_isotope(data) - - def _coerce_neutral_losses(self, data: Dict[str, str]) -> List: - return super()._coerce_neutral_losses(data) - - def _coerce_analyte_reference(self, data: Dict[str, str]) -> str: - return None - - def _dispatch_immonium(self, data: Dict[str, Any], adducts: List, charge: int, isotope: int, neutral_losses: List, - analyte_reference: Any, mass_error: Any, **kwargs): - modification = data['immonium_modification'] - if modification is not None: - try: - modification = MODIFICATION_NAME_MAP[modification] - data['immonium_modification'] = modification - except KeyError as err: - print(f"Failed to convert immonium ion modification {modification}") - return super(MSPAnnotationStringParser, self)._dispatch_immonium( - data, adducts, charge, isotope, neutral_losses, analyte_reference, mass_error, **kwargs) - - def _get_peptide_sequence_for_analyte(self, spectrum: Spectrum, analyte_reference: Optional[Any]=None) -> str: - if analyte_reference is None: - if len(spectrum.analytes) == 0: - return None - else: - analyte_reference = spectrum.analytes[FIRST_ANALYTE_KEY].id - analyte = spectrum.analytes.get(analyte_reference) - if analyte is None: - return None - return analyte.get_attribute('MS:1000888|stripped peptide sequence') - - -parse_annotation = MSPAnnotationStringParser(annotation_pattern) -MODIFICATION_LIST_PARSER = re.compile(r"(\d+),([ARNDCEQGHKMFPSTWYVIL_\-]),([A-Za-z0-9_\-]+)") - - -class ModificationParser: - pattern: re.Pattern - modification_map: Dict[str, str] - unknown_modifications: Set[str] - - def __init__(self, pattern: str=None, modification_map: Dict[str, str]=None): - if pattern is None: - pattern = MODIFICATION_LIST_PARSER.pattern - if modification_map is None: - modification_map = dict(MODIFICATION_NAME_MAP) - self.pattern = re.compile(pattern) - self.modification_map = modification_map - self.unknown_modifications = set() - - def __call__(self, text: str): - return self.parse(text) - - def parse(self, text: str) -> List[Tuple[int, str, str]]: - if not isinstance(text, str) or not text: - return [] - i = 0 - n = len(text) - - mods = [] - while i < n and text[i].isdigit(): - i += 1 - - for position, residue, mod in self.pattern.findall(text): - position = int(position) - if mod not in self.modification_map: - warnings.warn(f"{mod} is not found in the known MSP modification mapping. Using this name verbatim") - modification_name = mod - self.modification_map[mod] = mod - self.unknown_modifications.add(mod) - else: - modification_name = self.modification_map[mod] - mods.append((position, residue, modification_name)) - return mods - - -def null_handler(key: str, value: str, container: Attributed) -> bool: - return True - - -msp_spectrum_attribute_handler = DispatchingAttributeHandler() -msp_analyte_attribute_handler = DispatchingAttributeHandler() - - -msp_spectrum_attribute_handler.add(FunctionAttributeHandler("Nprot", null_handler)) -msp_spectrum_attribute_handler.add(FunctionAttributeHandler("Peptype", null_handler)) - - -@msp_spectrum_attribute_handler.add -@FunctionAttributeHandler.wraps("Spectrum_type") -def ms_level_handler(key: str, value: str, container: Attributed) -> bool: - attr_name = "MS:1000511|ms level" - if value is None: - return False - if isinstance(value, str): - if value.lower().startswith("ms"): - value = int(value[2:]) - container.add_attribute(attr_name, value) - return True - - -@msp_spectrum_attribute_handler.add -@FunctionAttributeHandler.wraps("ionmode", "ion_mode", "ionization mode", "IONMODE", "Ion_mode") -def polarity_handler(key: str, value: str, container: Attributed) -> bool: - polarity_term = "MS:1000465|scan polarity" - positive = "MS:1000130|positive scan" - negative = "MS:1000129|negative scan" - - if isinstance(value, str): - value = value.lower() - if value == 'positive': - value = positive - elif value == 'negative': - value = negative - else: - raise ValueError(f"Can't infer scan polarity from {value}") - container.add_attribute(polarity_term, value) - return True - return False - - -@msp_spectrum_attribute_handler.add -@FunctionAttributeHandler.wraps("HCD") -def dissociation_method_handler(key: str, value: str, container: Attributed) -> bool: - container.add_attribute("MS:1000044|dissociation method", - "MS:1000422|beam-type collision-induced dissociation") - found_match = False - if value is not None: - match = re.match(r"([\d\.]+)\s*ev", value, flags=re.IGNORECASE) - if match is not None: - found_match = True - group_identifier = container.get_next_group_identifier() - container.add_attribute("MS:1000045|collision energy", - try_cast(match.group(1)), group_identifier) - container.add_attribute("UO:0000000|unit", "UO:0000266|electronvolt", group_identifier) - match = re.match(r"([\d\.]+)\s*%", value) - if match is not None: - found_match = True - group_identifier = container.get_next_group_identifier() - container.add_attribute("MS:1000045|collision energy", - try_cast(match.group(1)), group_identifier) - container.add_attribute("UO:0000000|unit", "UO:0000187|percent", group_identifier) - return found_match - - -@msp_spectrum_attribute_handler.add -@FunctionAttributeHandler.wraps("Collision_energy", "CE", "colenergy", "collisionenergy", "ionization energy") -def collision_energy_handler(key: str, value: str, container: Attributed) -> bool: - if isinstance(value, str): - if "NCE" in value: - return normalized_collision_energy_handler(key, value, container) - match = re.match(r"([\d\.]+)", value) - if match is not None: - value = try_cast(match.group(1)) - if value is not None: - group_identifier = container.get_next_group_identifier() - container.add_attribute( - "MS:1000045|collision energy", value, group_identifier) - container.add_attribute( - "UO:0000000|unit", "UO:0000266|electronvolt", group_identifier) - return True - return False - - -@msp_spectrum_attribute_handler.add -@FunctionAttributeHandler.wraps("NCE", "nce") -def normalized_collision_energy_handler(key: str, value: str, container: Attributed) -> bool: - if isinstance(value, str): - match = re.match(r"([\d\.]+)", value) - if match is not None: - value = try_cast(match.group(1)) - if value is not None: - group_identifier = container.get_next_group_identifier() - container.add_attribute( - "MS:1000138|normalized collision energy", value, group_identifier) - container.add_attribute( - "UO:0000000|unit", "UO:0000187|percent", group_identifier) - return True - return False - - -@msp_spectrum_attribute_handler.add -@FunctionAttributeHandler.wraps("RT", "rettime", "retentiontime", "rtinseconds") -def rt_handler(key, value, container) -> bool: - match = re.match(r"([\d\.]+)\s*(\D*)", - value) - if match is not None: - if match.group(2): - container.add_attribute( - "ERROR", f"Need more RT parsing code to handle this value") - return False - else: - group_identifier = container.get_next_group_identifier() - container.add_attribute( - "MS:1000894|retention time", try_cast(match.group(1)), group_identifier) - #### If the value is greater than 250, assume it must be seconds - if float(match.group(1)) > 250 or key.lower() == 'rtinseconds': - container.add_attribute( - "UO:0000000|unit", "UO:0000010|second", group_identifier) - #### Although normally assume minutes - else: - container.add_attribute( - "UO:0000000|unit", "UO:0000031|minute", group_identifier) - return True - return False - - -@msp_spectrum_attribute_handler.add -@FunctionAttributeHandler.wraps("ms2IsolationWidth") -def isolation_width_handler(key, value, container) -> bool: - if value is None: - return False - group_identifier = container.get_next_group_identifier() - container.add_attribute("MS:1000828|isolation window lower offset", - (float(value) / 2), group_identifier) - container.add_attribute("UO:0000000|unit", - "MS:1000040|m/z", group_identifier) - group_identifier = container.get_next_group_identifier() - container.add_attribute("MS:1000829|isolation window upper offset", - (float(value) / 2), group_identifier) - container.add_attribute("UO:0000000|unit", - "MS:1000040|m/z", group_identifier) - return True - - -@msp_analyte_attribute_handler.add -@FunctionAttributeHandler.wraps("Mz_diff", "Theo_mz_diff") -def mz_diff_handler(key, value, container: Attributed) -> bool: - if isinstance(value, float): - # We must be dealing with a unit-less entry. - group_identifier = container.get_next_group_identifier() - container.add_attribute( - "MS:1001975|delta m/z", abs(value), group_identifier) - container.add_attribute( - "UO:0000000|unit", "MS:1000040|m/z", group_identifier) - else: - match = re.match( - r"([\-\+e\d\.]+)\s*ppm", value, flags=re.IGNORECASE) - if match is not None: - group_identifier = container.get_next_group_identifier() - container.add_attribute( - "MS:1001975|delta m/z", try_cast(match.group(1)), group_identifier) - container.add_attribute( - "UO:0000000|unit", "UO:0000169|parts per million", group_identifier) - else: - match = re.match( - r"([\-\+e\d\.]+)\s*", value) - if match is not None: - group_identifier = container.get_next_group_identifier() - container.add_attribute( - "MS:1001975|delta m/z", try_cast(match.group(1)), group_identifier) - container.add_attribute( - "UO:0000000|unit", "MS:1000040|m/z", group_identifier) - else: - return False - return True - - -@msp_spectrum_attribute_handler.add -@FunctionAttributeHandler.wraps("Dev_ppm") -def dev_ppm_handler(key, value, container) -> bool: - if value is None: - return False - group_identifier = container.get_next_group_identifier() - container.add_attribute( - "MS:1001975|delta m/z", try_cast(value), group_identifier) - container.add_attribute( - "UO:0000000|unit", "UO:0000169|parts per million", group_identifier) - return True - - -@msp_spectrum_attribute_handler.add -@FunctionAttributeHandler.wraps("Nrep", "Nreps") -def nreps_handler(key, value, container): - if value is None: - return False - if not isinstance(value, str): - value = str(value) - match = re.match( - r"(\d+)/(\d+)", value) - if match is not None: - container.add_attribute( - "MS:1003070|number of replicate spectra used", try_cast(match.group(1))) - container.add_attribute( - "MS:1003069|number of replicate spectra available", try_cast(match.group(2))) - return True - else: - match = re.match( - r"(\d+)", value) - if match is not None: - container.add_attribute( - "MS:1003070|number of replicate spectra used", try_cast(match.group(1))) - container.add_attribute( - "MS:1003069|number of replicate spectra available", try_cast(match.group(1))) - return True - else: - return False - - -@msp_analyte_attribute_handler.add -@FunctionAttributeHandler.wraps("Organism") -def organism_handler(key, value, container): - if value is None: - return False - value = value.strip('"') - - if value in species_map: - group_identifier = container.get_next_group_identifier() - for item in species_map[value]: - container.add_attribute( - item[0], try_cast(item[1]), group_identifier) - return True - return False - - -@msp_analyte_attribute_handler.add -@FunctionAttributeHandler.wraps("Protein") -def protein_handler(key, value, container: Attributed): - if value is None: - return False - key = "MS:1000885|protein accession" - match = re.match(r"\(pre=(.),post=(.)\)", value) - group_identifier = None - if match is not None: - value = value[:match.start()] - group_identifier = container.get_next_group_identifier() - container.add_attribute("MS:1001112|n-terminal flanking residue", - match.group(1), group_identifier=group_identifier) - container.add_attribute("MS:1001113|c-terminal flanking residue", - match.group(2), group_identifier=group_identifier) - container.add_attribute(key, re.sub(r"\(pre=(.),post=(.)\)", '', value.strip('"').strip("'")), - group_identifier=group_identifier) - return True - - -@msp_spectrum_attribute_handler.add -@FunctionAttributeHandler.wraps("BasePeak") -def base_peak_handler(key, value, container: Attributed): - if value is None: - return False - value = float(value) - group_id = container.get_next_group_identifier() - container.add_attribute("MS:1000505|base peak intensity", value, group_id) - container.add_attribute("UO:0000000|unit", "MS:1000131|number of detector counts", group_id) - return True - - -class _UnknownTermTracker: - counts: DefaultDict - - def add(self, key: str, value: Optional[str]=None): - """Add an unknown attribute to the tracker""" - raise NotImplementedError() - - def items(self): - return self.counts.items() - - -class UnknownKeyValueTracker(_UnknownTermTracker): - """ - A diagnostic tool for tracking attributes with values that the parser doesn't know how to interpret. - - This tracker holds both keys and values, and can grow quite large. For debugging purposes only. - """ - - def __init__(self) -> None: - self.counts = DefaultDict(lambda: DefaultDict(int)) - - def add(self, key: str, value: Optional[str]=None): - self.counts[key][value] += 1 - - -class UnknownKeyTracker(_UnknownTermTracker): - """A diagnostic tool for tracking attributes that the parser doesn't know how to interpret.""" - - def __init__(self) -> None: - self.counts = DefaultDict(int) - - def add(self, key: str, value: Optional[str] = None): - self.counts[key] += 1 - - -protein_attributes_to_group = [ - "MS:1003048|number of enzymatic termini", - "MS:1001045|cleavage agent name", - "MS:1001112|n-terminal flanking residue", - "MS:1001113|c-terminal flanking residue", - "MS:1003044|number of missed cleavages", - "MS:1000885|protein accession", -] - - -class MSPSpectralLibrary(_PlainTextSpectralLibraryBackendBase): - """ - A reader for the plain text NIST MSP spectral library format. - - The MSP format is only roughly defined, and does places few - constraints on the meanings of spectrum attributes. This parser - attempts to cover a variety of different ways that MSPs found - "in the wild" have denoted different spectrum properties, but - is neither exhaustive nor nuanced enough to know from context - exactly what those files' authors intended, making a best guess - at when they correspond to in the controlled vocabulary mapping - for :mod:`mzlib` - - - Attributes - ---------- - modification_parser : :class:`ModificationParser` - A parser for peptide modifications - unknown_attributes : :class:`_UnknownTermTracker` - A tracker for unknown attributes. Used to tell how much information - the reader is unable to map onto the controlled vocabulary. - """ - - file_format = "msp" - format_name = "msp" - - modification_parser: ModificationParser - unknown_attributes: _UnknownTermTracker - - def __init__(self, filename, index_type=None, read_metadata=True, create_index: bool=True): - super().__init__(filename, index_type, read_metadata, create_index=create_index) - self.modification_parser = ModificationParser() - self.unknown_attributes = UnknownKeyTracker() - - @classmethod - def guess_from_header(cls, filename: str) -> bool: - with open_stream(filename, 'r') as stream: - first_line = stream.readline() - if leader_terms_pattern.match(first_line): - return True - return False - - def read_header(self) -> bool: - filename = self.filename - file_like_object = isinstance(filename, io.IOBase) - - stream = open_stream(filename, 'rt') - match, offset = self._parse_header_from_stream(stream) - if file_like_object: - if stream.seekable(): - stream.seek(0) - stream.detach() - else: - stream.close() - return match - - def _parse_header_from_stream(self, stream: io.IOBase) -> Tuple[bool, int]: - first_line = stream.readline() - if isinstance(first_line, bytes): - first_line = first_line.decode('utf8') - attributes = AttributeManager() - attributes.add_attribute(FORMAT_VERSION_TERM, DEFAULT_VERSION) - if isinstance(self.filename, (str, os.PathLike)): - attributes.add_attribute(LIBRARY_NAME_TERM, self.filename.rsplit('.msp', 1)[0].split(os.sep)[-1]) - elif hasattr(stream, 'name'): - attributes.add_attribute(LIBRARY_NAME_TERM, stream.name.rsplit('.msp', 1)[0].split(os.sep)[-1]) - self.attributes.clear() - self.attributes._from_iterable(attributes) - if leader_terms_pattern.match(first_line): - return True, 0 - return False, 0 - - def create_index(self) -> int: - """ - Populate the spectrum index - - Returns - ------- - n_spectra: int - The number of entries read - """ - #### Check that the spectrum library filename isvalid - filename = self.filename - - begin_loc = None - file_like_object = False - #### Determine the filesize - try: - file_size = os.path.getsize(filename) - except TypeError: - if isinstance(filename, io.IOBase): - file_like_object = True - if filename.seekable(): - begin_loc = filename.tell() - filename.seek(0, os.SEEK_END) - file_size = filename.tell() - filename.seek(0) - infile = open_stream(filename, 'r') - - state = 'header' - spectrum_buffer = [] - n_spectra = 0 - start_index = 0 - file_offset = 0 - line_beginning_file_offset = 0 - spectrum_file_offset = 0 - spectrum_name = '' - - # Required for counting file_offset manually (LF vs CRLF) - infile.readline() - file_offset_line_ending = len(infile.newlines) - 1 - infile.seek(0) - - # if debug: - # eprint("INFO: Reading..", end='', flush=True) - logger.debug(f"Reading {filename} ({file_size} bytes)...") - while 1: - line = infile.readline() - if len(line) == 0: - break - - line_beginning_file_offset = file_offset - - #### tell() is twice as slow as counting it myself - # file_offset = infile.tell() - file_offset += len(line) + file_offset_line_ending - - line = line.rstrip() - # TODO: Name: could be Compound or SpectrumName - if state == 'header': - if leader_terms_pattern.match(line): - state = 'body' - spectrum_file_offset = line_beginning_file_offset - else: - continue - if state == 'body': - if len(line) == 0: - continue - if leader_terms_pattern.match(line): - if len(spectrum_buffer) > 0: - self.index.add( - number=n_spectra + start_index, - offset=spectrum_file_offset, - name=spectrum_name, - analyte=None) - n_spectra += 1 - spectrum_buffer = [] - #### Commit every now and then - if n_spectra % 10000 == 0: - self.index.commit() - logger.info(f"... Indexed {file_offset} bytes, {n_spectra} spectra read") - - spectrum_file_offset = line_beginning_file_offset - spectrum_name = leader_terms_line_pattern.match(line).group(1) - - spectrum_buffer.append(line) - logger.debug(f"Processed {file_offset} bytes, {n_spectra} spectra read") - self.index.add( - number=n_spectra + start_index, - offset=spectrum_file_offset, - name=spectrum_name, - analyte=None) - self.index.commit() - n_spectra += 1 - - #### Flush the index - self.index.commit() - - if not file_like_object: - infile.close() - else: - infile.detach() - if begin_loc is not None: - filename.seek(begin_loc) - return n_spectra - - def _buffer_from_stream(self, infile: Iterable[str]) -> List[str]: - state = 'body' - spectrum_buffer = [] - - file_offset = 0 - line_beginning_file_offset = 0 - for line in infile: - line_beginning_file_offset = file_offset - file_offset += len(line) - line = line.rstrip() - if state == 'body': - if len(line) == 0: - continue - if leader_terms_pattern.match(line): - if len(spectrum_buffer) > 0: - return spectrum_buffer - spectrum_buffer.append(line) - return spectrum_buffer - - def _parse(self, buffer: Iterable[str], spectrum_index: int=None) -> Spectrum: - - #### Start in the header section of the entry - in_header = True - - #### Reset all spectrum properties in case there is already data here - attributes = {} - peak_list = [] - - #### Loop through each line in the buffered list - for line in buffer: - - #print(line) - - #### If in the the header portion of the entry - if in_header: - - #### Extract the key,value pair by splitting on the *first* colon with optional whitespace - match = re.match(r"\s*#", line) - if match: - continue - elif line.count(":") > 0: - key, value = re.split(r":\s*", line, 1) - attributes[key] = value - elif line.count("=") > 0: - key, value = re.split(r"=\s*", line, 1) - attributes[key] = value - elif line.count("\t") > 0: - warnings.warn(f"Line {line!r} looks like a peak annotation?") - in_header = False - else: - key = line - value = None - attributes[key] = value - - - #### If the key is "Num peaks" then we're done with the header and peak list follows - if key in NUM_PEAKS_KEYS: - in_header = False - - #### The "Comment" key requires special parsing - if key == "Comment" or key == "Comments": - - #### Remove it from attributes - del attributes[key] - self._parse_comment(value, attributes) - - #### Else in the peaks section. Parse the peaks. - else: - #### Split into the expected three values - values = re.split(r'\s+', line, maxsplit=2) - # Sometimes MSP files have multiple peaks on the same line, delimited by ';', - # so we must potentially parse more than one peak per line. - if values[1].endswith(";"): - buffered_peaks = [] - buffered_peaks.append(values[:2]) - buffered_peaks[0][1] = buffered_peaks[0][1].strip(";") - rest = values[0] - for block in re.split(r";\s?", rest): - if block: - buffered_peaks.append(re.split(r'\s+', block, maxsplit=2)) - - else: - buffered_peaks = [values] - - for values in buffered_peaks: - interpretations = "" - aggregation = "" - if len(values) == 1: - mz = values - intensity = "1" - if len(values) == 2: - mz, intensity = values - elif len(values) == 3: - mz, intensity, interpretations = values - elif len(values) > 3: - mz, intensity, interpretations = values[0:2] - else: - mz = "1" - intensity = "1" - - interpretations = interpretations.strip('"') - if interpretations.startswith("?"): - parts = re.split(r"\s+", interpretations) - if len(parts) > 1: - # Some msp files have a concept for ?i, but this requires a definition - interpretations = "?" - aggregation = parts[1:] - else: - if " " in interpretations: - parts = re.split(r"\s+", interpretations) - interpretations = parts[0] - aggregation = parts[1:] - - #### Add to the peak list - peak_list.append([float(mz), float(intensity), interpretations, aggregation]) - - #### Now convert the format attributes to standard ones - spectrum = self._make_spectrum(peak_list, attributes) - if spectrum_index is not None: - spectrum.index = spectrum_index - else: - spectrum.index = -1 - spectrum.key = spectrum.index + 1 - has_observation_freq = (False, 0) - for i, peak in enumerate(spectrum.peak_list): - try: - parsed_interpretation = self._parse_annotation(peak[2], spectrum=spectrum) - except ValueError as err: - message = str(err) - raise ValueError( - f"An error occurred while parsing the peak annotation for peak {i}: {message}") from err - - if parsed_interpretation and isinstance(parsed_interpretation[0], annotation.InvalidAnnotation) and peak[3]: - logger.debug("Failed to parse interpretation string %r with assumed %d aggregation fields, trying to parse the combined string", - peak[2], len(peak[3])) - - peak[2] = " ".join([peak[2]] + peak[3]) - peak[3] = [] - try: - parsed_interpretation = self._parse_annotation(peak[2], spectrum=spectrum) - except ValueError as err: - message = str(err) - raise ValueError( - f"An error occurred while parsing the peak annotation for peak {i}: {message}") from err - - peak[2] = parsed_interpretation - for i, agg in enumerate(peak[3]): - # NOTE: Making the potentially unsafe assumption that the only fractional - # aggregation statistic is the peak frequency. At this time, we haven't formalized - # any other aggregation metric that I also have an MSP example for. - if '/' in agg: - try: - agg = _parse_fraction(agg) - peak[3][i] = agg - has_observation_freq = (True, i) - except ValueError: - pass - except Exception as err: - raise ValueError(f"An error occurred while parsing the peak aggregation for peak {i}: {str(err)}") from err - - aggregation_metrics = [] - if has_observation_freq[0]: - aggregation_metrics.append((PEAK_ATTRIB, PEAK_OBSERVATION_FREQ)) - - if aggregation_metrics: - spectrum.add_attribute_group(aggregation_metrics) - - return spectrum - - def _parse_annotation(self, annotation: str, wrap_errors: bool=True, **kwargs): - return parse_annotation(annotation_string=annotation, wrap_errors=wrap_errors, **kwargs) - - def _parse_comment(self, value: str, attributes: Attributed): - comment_items = re.split(" ", value) - - #### Any spaces within quotes are then de-split - fixed_comment_items = [] - quote_counter = 0 - new_item = "" - for item in comment_items: - if new_item > "": - new_item = new_item + " " - new_item = new_item + item - n_quotes = new_item.count('"') - if n_quotes % 2 == 0: - fixed_comment_items.append(new_item) - new_item = "" - - #### Try to split each item on the first = character and store in attributes - for item in fixed_comment_items: - #### If there is an = then split on the first one and store key and value - if item.count("=") > 0: - comment_key, comment_value = item.split("=", 1) - cleaned_key = comment_key.strip('"') - if len(cleaned_key) != len(comment_key): - comment_value = comment_value.strip('"') - attributes[cleaned_key] = try_cast(comment_value) - - #### Otherwise just store the key with a null value - else: - attributes[item] = None - - def _make_attribute_handlers(self): - """ - Create the attribute handling scopes that map this flavor of MSP's - attributes onto controlled vocabulary terms in context. - - This method should be overridden in sub-classes to allow them - to change the meanings of attributes, add new ones, or otherwise - redirect how they are interpreted. - - See the :class:`AttributeHandler` type tree for more details about - how the distributed predicates are resolved. - - Returns - ------- - other_manager : :class:`AttributeHandler` - The attribute handler for uncategorized attributes that will be added - to a :class:`Spectrum`. - analyte_manager : :class:`AttributeHandler` - The attribute handler for attributes that will be added to a :class:`Analyte` - interpretation_manager : :class:`AttributeHandler` - The attribute handler for attributes that will be added to a :class:`Interpretation` - interpretation_member_manager : :class:`AttributeHandler` - The attribute handler for attributes that will be added to a :class:`InterpretationMember` - spectrum_manager : :class:`AttributeHandler` - The attribute handler for attributes that will be added to a :class:`Spectrum` - analyte_fallback_manager : :class:`AttributeHandler` - The attribute handler for attributes that will be tried for any attribute - that fails to be categorized by all of the other managers to be added to the - :class:`Analyte` before labeling the attribute as "unknown". - """ - other_manager = MappingAttributeHandler(other_terms) - analyte_manager = MappingAttributeHandler(analyte_terms) - interpretation_manager = MappingAttributeHandler(interpretation_terms) - interpretation_member_manager = MappingAttributeHandler(interpretation_member_terms) - return (other_manager, - analyte_manager, - interpretation_manager, - interpretation_member_manager, - msp_spectrum_attribute_handler, - msp_analyte_attribute_handler) - - def _make_spectrum(self, peak_list: List, attributes: Mapping[str, str]): - spectrum = self._new_spectrum() - interpretation = self._new_interpretation(FIRST_INTERPRETATION_KEY) - interpretation_member = None - analyte = self._new_analyte(FIRST_ANALYTE_KEY) - spectrum.add_analyte(analyte) - # interpretation.add_analyte(analyte) - spectrum.peak_list = peak_list - # spectrum.interpretations.add_interpretation(interpretation) - - #### Add special terms that we want to start off with - for term in leader_terms: - if term in attributes: - spectrum.add_attribute( - leader_terms[term], try_cast(attributes[term])) - break - else: - spectrum.add_attribute( - "ERROR", f"Required term {leader_terms[term]} is missing") - - #### Translate the rest of the known attributes and collect unknown ones - unknown_terms = [] - - (other_manager, analyte_manager, interpretation_manager, interpretation_member_manager, - spectrum_func_handler, analyte_func_handler) = self._make_attribute_handlers() - for attribute in attributes: - - #### Skip a leader term that we already processed - if attribute in leader_terms: - continue - if not attribute: - continue - if attribute in other_manager: - if not other_manager(attribute, attributes[attribute], spectrum): - unknown_terms.append(attribute) - - elif attribute in analyte_manager: - if not analyte_manager(attribute, attributes[attribute], analyte): - unknown_terms.append(attribute) - - elif attribute in interpretation_manager: - if not interpretation_manager(attribute, attributes[attribute], interpretation): - unknown_terms.append(attribute) - - elif attribute in interpretation_member_manager: - if interpretation_member is None: - interpretation_member = self._new_interpretation_member(1) - interpretation.add_member_interpretation(interpretation_member) - if not interpretation_member_manager(attribute, attributes[attribute], interpretation_member): - unknown_terms.append(attribute) - - elif attribute in spectrum_func_handler: - if not spectrum_func_handler(attribute, attributes[attribute], spectrum): - unknown_terms.append(attribute) - - elif attribute in analyte_func_handler: - if not analyte_func_handler(attribute, attributes[attribute], analyte): - unknown_terms.append(attribute) - - #### Expand the Fullname attribute - elif attribute == "Fullname": - if attributes[attribute] is not None: - match = re.match( - r"([A-Z\-\*])\.([A-Z]+)\.([A-Z\-\*])/*([\d]*)", attributes[attribute]) - if match is not None: - analyte.add_attribute( - "MS:1000888|stripped peptide sequence", match.group(2)) - analyte.add_attribute( - "MS:1001112|n-terminal flanking residue", match.group(1)) - analyte.add_attribute( - "MS:1001113|c-terminal flanking residue", match.group(3)) - if match.group(4): - analyte.add_attribute( - "MS:1000041|charge state", try_cast(match.group(4))) - else: - spectrum.add_attribute( - "ERROR", f"Unable to parse {attributes[attribute]} in {attribute}") - unknown_terms.append(attribute) - else: - spectrum.add_attribute( - "ERROR", f"Attribute {attribute} must have a value") - unknown_terms.append(attribute) - - #### Otherwise add this term to the list of attributes that we don't know how to handle - else: - unknown_terms.append(attribute) - - if not analyte.has_attribute(STRIPPED_PEPTIDE_TERM): - if spectrum.has_attribute(SPECTRUM_NAME): - name = spectrum.get_attribute(SPECTRUM_NAME) - if name: - match = re.match(r"([ARNDCEQGHKMFPSTWYVIL]+)/(\d+)", name) - if match: - analyte.add_attribute( - STRIPPED_PEPTIDE_TERM, match.group(1)) - analyte.add_attribute( - "MS:1000041|charge state", try_cast(match.group(2))) - - #### Handle the uninterpretable terms - for attribute in unknown_terms: - self.unknown_attributes.add(attribute, attributes[attribute]) - if attributes[attribute] is None: - spectrum.add_attribute( - "MS:1003275|other attribute name", try_cast(attribute)) - else: - group_identifier = spectrum.get_next_group_identifier() - spectrum.add_attribute( - "MS:1003275|other attribute name", try_cast(attribute), group_identifier) - spectrum.add_attribute("MS:1003276|other attribute value", - try_cast(attributes[attribute]), group_identifier) - - self._complete_analyte(analyte) - - if analyte: - spectrum.add_analyte(analyte) - interpretation.add_analyte(analyte) - spectrum.add_interpretation(interpretation) - return spectrum - - def _deduplicate_attr(self, container: Attributed, attribute_name: str) -> int: - try: - attrs = container.get_attribute(attribute_name, raw=True) - except KeyError: - return 0 - if isinstance(attrs, list): - # Sometimes there are multiple entries that map to molecular mass, and one is the nominal - # mass. Prefer listing the most precise mass first. Apply the same logic to all attributes. - attrs.sort(key=lambda x: len(str(x.value)), reverse=True) - container.remove_attribute(attrs[0].key) - seen_values = set() - for attr in attrs: - key = (attr.value, attr.group_id) - if key in seen_values: - continue - seen_values.add(key) - container.add_attribute(attr.key, attr.value, attr.group_id) - return len(attrs) - len(seen_values) - return 0 - - def _complete_analyte(self, analyte: Analyte): - if analyte.has_attribute(STRIPPED_PEPTIDE_TERM): - peptide = proforma.ProForma.parse(analyte.get_attribute(STRIPPED_PEPTIDE_TERM)) - if analyte.has_attribute(PEPTIDE_MODIFICATION_TERM): - modification_details = analyte.get_attribute(PEPTIDE_MODIFICATION_TERM) - mods = self.modification_parser(modification_details) - for position, residue, mod in mods: - if position == 0 and mod in TERMINAL_MODIFICATIONS: - peptide.n_term = [proforma.GenericModification(mod)] - else: - seqpos = list(peptide.sequence[position]) - if not seqpos[1]: - seqpos[1] = [proforma.GenericModification(mod)] - peptide.sequence[position] = tuple(seqpos) - assert seqpos[0] == residue - analyte.add_attribute("MS:1003169|proforma peptidoform sequence", str(peptide)) - if analyte.has_attribute(PEPTIDE_MODIFICATION_TERM): - analyte.remove_attribute(PEPTIDE_MODIFICATION_TERM) - analyte.add_attribute("MS:1001117|theoretical mass", peptide.mass) - - self._pack_protein_description(analyte) - - self._deduplicate_attr(analyte, "MS:1000224|molecular mass") - self._deduplicate_attr(analyte, "MS:1000866|molecular formula") - - def _pack_protein_description(self, analyte: Analyte): - table = {} - max_len = 0 - - # Collect terms that describe a protein - for term in protein_attributes_to_group: - if not analyte.has_attribute(term): - table[term] = [] - continue - values = analyte.get_attribute(term, raw=True) - if not isinstance(values, list): - values = [values] - max_len = max(max_len, len(values)) - table[term] = values - - # Ensure that all arrays are the same length - for k, v in table.items(): - if len(v) < max_len: - v.extend([None] * (max_len - len(v))) - - # Group together terms and remove the previous entries - groups = [] - for i in range(max_len): - group = [] - for k, v in table.items(): - if v[i] is None: - continue - group.append((k, v[i].value)) - analyte.remove_attribute(v[i].key, v[i].group_id) - groups.append(group) - - # Now add back the groups - for group in groups: - analyte.add_attribute_group(group) - - def get_spectrum(self, spectrum_number: int=None, spectrum_name: str=None) -> Spectrum: - # keep the two branches separate for the possibility that this is not possible with all - # index schemes. - if spectrum_number is not None: - if spectrum_name is not None: - raise ValueError("Provide only one of spectrum_number or spectrum_name") - index_record = self.index.record_for(spectrum_number) - offset = index_record.offset - elif spectrum_name is not None: - index_record = self.index.record_for(spectrum_name) - spectrum_number = index_record.number - offset = index_record.offset - else: - raise ValueError("Must provide either spectrum_number or spectrum_name argument") - buffer = self._get_lines_for(offset) - spectrum = self._parse(buffer, index_record.index) - return spectrum - - def summarize_parsing_errors(self) -> Dict: - errors = super().summarize_parsing_errors() - errors['unknown attributes'] = DefaultDict(dict) - for k, v in self.unknown_attributes.items(): - errors['unknown attributes'][k] = v - return errors - - -def _parse_fraction(x: str) -> float: - a, b = x.split("/") - return int(a) / int(b) - - -class MSPSpectralLibraryWriter(SpectralLibraryWriterBase): - file_format = "msp" - - analyte_keys = { - "MS:1000866|molecular formula": "Formula", - "MS:1003044|number of missed cleavages": "MC", - "MS:1001471|peptide modification details": "Mods", - "MS:1003043|number of residues": "Naa", - "MS:1003208|experimental precursor monoisotopic m/z": "PrecursorMonoisoMZ", - "MS:1003054|theoretical average m/z": "Mz_av", - "MS:1003169|proforma peptidoform sequence": "ProForma", - "MS:1000888|stripped peptide sequence": "Peptide", - "MS:1000041|charge state": "Charge", - } - - for species_name, keys in species_map.items(): - analyte_keys[tuple(keys[0])] = ("Organism", species_name) - - modification_map = {v: k for k, v in MODIFICATION_NAME_MAP.items()} - - spectrum_keys = { - "MS:1000041|charge state": "Charge", - ("MS:1003065|spectrum aggregation type", "MS:1003066|singleton spectrum"): "Single", - ("MS:1003065|spectrum aggregation type", "MS:1003067|consensus spectrum"): "Consensus", - "MS:1003057|scan number": "Scan", - "MS:1003203|constituent spectrum file": "Origfile", - "MS:1000002|sample name": "Sample", - "MS:1000512|filter string": "Filter", - "MS:1003086|precursor apex intensity": "Precursor1MaxAb", - "MS:1009013|isolation window precursor purity": "Purity", - "MS:1000505|base peak intensity": "BasePeak", - "MS:1002599|splash key": "Splash", - "MS:1003289|intensity of highest unassigned peak": "max_unassigned_ab", - "MS:1003080|top 20 peak unassigned intensity fraction": "Unassigned", - "MS:1003079|total unassigned intensity fraction": "Unassign_all", - "MS:1003290|number of unassigned peaks among top 20 peaks": "top_20_num_unassigned_peaks", - ("MS:1000044|dissociation method", "MS:1000422|beam-type collision-induced dissociation"): "HCD", - ("MS:1000044|dissociation method", "MS:1002472|trap-type collision-induced dissociation"): "CID", - } - - # TODO: add these - interpretation_keys = { - "MS:1002354|PSM-level q-value": "Q-value", - } - - def __init__(self, filename, **kwargs): - super(MSPSpectralLibraryWriter, self).__init__(filename) - self._coerce_handle(self.filename) - - def write_header(self, library: SpectralLibraryBackendBase): - pass - - def write_attribute_set(self, attribute_set: AttributeSet, attribute_set_type: AttributeSetTypes): - pass - - def _format_value(self, value): - if isinstance(value, str): - if not (value.startswith('"') and value.endswith('"')): - value = f"\"{value}\"" - return str(value) - - def _proforma_to_mods(self, proforma_seq: str) -> str: - parsed = proforma.ProForma.parse(proforma_seq) - mods = [(i, tok) for i, tok in enumerate(parsed) if tok[1]] - if mods: - tokens = [] - for i, mod_site in mods: - tokens.append(str(i)) - tokens.append(mod_site[0]) - mod = mod_site[1][0] - mod_name = self.modification_map.get(mod.name, mod.name) - tokens.append(mod_name) - return f'Mods={len(mods)}({",".join(tokens)})' - else: - return 'Mods=0' - - def _protein_to_comments(self, analyte: Analyte) -> List[str]: - acc = [] - protein: ProteinDescription - for protein in analyte.proteins: - accession = None - pre = None - post = None - if protein.accession: - accession = protein.accession - if protein.flanking_n_terminal_residue: - pre = protein.flanking_n_terminal_residue - if protein.flanking_c_terminal_residue: - post = protein.flanking_c_terminal_residue - if accession: - token = accession - if token.startswith('"'): - token = token.strip('"') - if pre or post: - token += f"(pre={pre or '-'},post={post or '-'})" - acc.append(f"Protein={self._format_value(token)}") - if protein.number_of_enzymatic_termini == 2: - if protein.cleavage_agent == "MS:1001251|Trypsin": - acc.append("Pep=Tryptic") - elif protein.number_of_enzymatic_termini == 1: - if protein.cleavage_agent == "MS:1001251|Trypsin": - acc.append("Pep=SemiTryptic") - if protein.missed_cleavages is not None: - acc.append(f"MC={self._format_value(protein.missed_cleavages)}") - break - return acc - - def _build_comments(self, spectrum: Spectrum, attribute_container: Attributed, - rule_map: Dict) -> List[Tuple[str, str]]: - accumulator = [] - - for attr_name, msp_name in rule_map.items(): - if isinstance(attr_name, tuple): - if attribute_container.has_attribute(attr_name[0]): - value = attribute_container.get_attribute(attr_name[0]) - if value == attr_name[1]: - if isinstance(msp_name, str): - accumulator.append(msp_name) - elif isinstance(msp_name, (list, tuple)) and len(msp_name) == 2: - accumulator.append('='.join(msp_name)) - else: - raise TypeError(f"Can't infer conversion for {msp_name} given {attr_name}") - elif attribute_container.has_attribute(attr_name): - value = attribute_container.get_attribute(attr_name) - if isinstance(value, list): - logger.warn( - "Spectrum %r contains multiple values for %r, only the first will be saved", - spectrum.name, attr_name - ) - accumulator.append(f"{msp_name}={self._format_value(value[0])}") - else: - accumulator.append(f"{msp_name}={self._format_value(value)}") - return accumulator - - def build_spectrum_comments(self, spectrum: Spectrum) -> List[Tuple[str, str]]: - accumulator = self._build_comments(spectrum, spectrum, self.spectrum_keys) - if spectrum.analytes: - analyte = spectrum.get_analyte('1') - accumulator += self._build_comments(spectrum, analyte, self.analyte_keys) - if analyte.peptide: - accumulator.append(self._proforma_to_mods(analyte.peptide)) - accumulator += self._protein_to_comments(analyte) - if spectrum.interpretations: - interp = spectrum.get_interpretation('1') - accumulator += self._build_comments( - spectrum, interp, self.interpretation_keys) - return accumulator - - def write_spectrum(self, spectrum: Spectrum): - if len(spectrum.analytes) > 1: - logger.warning( - "Spectrum %r contains multiple analytes, MSP will only contain the first", - spectrum.name - ) - analyte = spectrum.get_analyte('1') - self.handle.write(f"Name: {spectrum.name}\n") - self.handle.write(f"MW: {analyte.mass}\n") - self.handle.write(f"Comment: {' '.join(self.build_spectrum_comments(spectrum))}\n") - self._write_peaks(spectrum) - self.handle.write("\n") - - def _format_annotation(self, annot: annotation.IonAnnotationBase): - parts = [] - if isinstance(annot, annotation.PeptideFragmentIonAnnotation): - parts.append(f"{annot.series}{annot.position}") - elif isinstance(annot, annotation.ImmoniumIonAnnotation): - parts.append(f"I{annot.amino_acid}{annot.modification if annot.modification else ''}") - elif isinstance(annot, annotation.ReporterIonAnnotation): - parts.append(annot.reporter_label) - if not parts: - return "?" - if annot.neutral_losses: - f = annotation.combine_formula(annot.neutral_losses) - if f[0] not in ('-', '+'): - f = '+' + f - parts.append(f) - if annot.adducts: - parts.append(f"[{annotation.combine_formula(annot.adducts)}]") - if annot.charge > 1: - parts.append(f"^{annot.charge}") - if annot.isotope: - if annot.isotope > 0: - parts.append(f'+{annot.isotope}i') - else: - parts.append(f'{annot.isotope}i') - if annot.mass_error: - parts.append(f'/{annot.mass_error}') - return ''.join(parts) - - def _write_peaks(self, spectrum: Spectrum): - self.handle.write(f"Num peaks: {len(spectrum.peak_list)}\n") - for peak in spectrum.peak_list: - annot = self._format_annotation(peak[2][0]) if peak[2] else '?' - self.handle.write(f"{peak[0]:0.4f}\t{peak[1]:0.4f}\t\"{annot}\"\n") - - def close(self): - self.handle.close() diff --git a/implementations/python/mzlib/backends/spectronaut.py b/implementations/python/mzlib/backends/spectronaut.py deleted file mode 100644 index 7af95b8..0000000 --- a/implementations/python/mzlib/backends/spectronaut.py +++ /dev/null @@ -1,299 +0,0 @@ -import json -import os - -from typing import List, Tuple, Dict, Iterator, Any, Deque, Union - -from pyteomics import proforma - -from mzlib import annotation -from mzlib.analyte import Analyte -from mzlib.backends.base import LIBRARY_NAME_TERM, _CSVSpectralLibraryBackendBase, FORMAT_VERSION_TERM, DEFAULT_VERSION -from mzlib.backends.utils import open_stream, urlify -from mzlib.spectrum import Spectrum, SPECTRUM_NAME - - -CHARGE_STATE = "MS:1000041|charge state" -SELECTED_ION_MZ = "MS:1003208|experimental precursor monoisotopic m/z" -SOURCE_FILE = "MS:1003203|constituent spectrum file" -STRIPPED_PEPTIDE_TERM = "MS:1000888|stripped peptide sequence" -PROFORMA_PEPTIDE_TERM = "MS:1003169|proforma peptidoform sequence" - -CUSTOM_ATTRIBUTE_NAME = "MS:1003275|other attribute name" -CUSTOM_ATTRIBUTE_VALUE = "MS:1003276|other attribute value" - -ID_SEP = "/" -_ID_SEP = ID_SEP.encode("ascii") - -NO_LOSS = 'noloss' - - -def _rewrite_modified_peptide_as_proforma(sequence: str) -> str: - if sequence.startswith("_"): - sequence = sequence.strip("_") - buffer: Deque[str] = Deque() - last_paren = None - for i, c in enumerate(sequence): - if c == ']': - # Erase any text in parentheses as these indicate the modification - # rule and not the modificatin name. We could look at the modification - # rule to infer N-term and C-term rules, but we don't have enough examples - if last_paren is not None: - k = i - last_paren - for _ in range(k + 1): - buffer.pop() - last_paren = None - buffer.append(c) - elif c == '(': - last_paren = i - buffer.append(c) - else: - buffer.append(c) - pf_seq = ''.join(buffer) - # A peptide with an N-terminal modification will start with a square brace - # but needs to have a "-" added to be well-formed ProForma - if pf_seq.startswith("["): - i = pf_seq.find(']') + 1 - if i == 0: - raise ValueError(f"Malformed peptide sequence {sequence}") - pf_seq = f"{pf_seq[:i]}-{pf_seq[i:]}" - return pf_seq - - -def _parse_value(value: str) -> Union[float, int, str, bool]: - try: - return json.loads(value) - except json.JSONDecodeError: - lower = value.lower() - if lower == "true": - return True - elif lower == "false": - return False - return value - - -class SpectronautTSVSpectralLibrary(_CSVSpectralLibraryBackendBase): - format_name = "spectronaut.tsv" - - _custom_spectrum_keys = [ - "ExcludeFromAssay", - "BGSInferenceId", - "AllowForNormalization", - "Workflow", - ] - - _custom_analyte_keys = [ - "IsProteotypic", - "FASTAName", - "Database", - "ProteinGroups", - ] - - _key_columns = ['ModifiedPeptide', 'PrecursorCharge'] - - _required_columns = ['PrecursorMz', 'PrecursorCharge', - 'ModifiedPeptide', 'StrippedPeptide', - 'FragmentMz', 'RelativeIntensity', - 'FragmentType', 'FragmentNumber', - 'FragmentCharge', 'FragmentLossType'] - - def __init__(self, filename: str, index_type=None, **kwargs): - super().__init__(filename, index_type=index_type, delimiter='\t', **kwargs) - - def _spectrum_type(self): - key = "MS:1003072|spectrum origin type" - value = "MS:1003073|observed spectrum" - return key, value - - def read_header(self) -> bool: - result = super().read_header() - self.add_attribute(FORMAT_VERSION_TERM, DEFAULT_VERSION) - if hasattr(self.filename, 'name'): - name = self.filename.name.replace(".gz", '').rsplit('.', 1)[0].split(os.sep)[-1] - else: - name = self.filename.replace(".gz", '').rsplit(".", 1)[0].split(os.sep)[-1] - self.add_attribute(LIBRARY_NAME_TERM, name) - self.add_attribute("MS:1003207|library creation software", "MS:1001327|Spectronaut") - return result - - def _batch_rows(self, iterator: Iterator[Dict[str, Any]]) -> Iterator[List[Dict[str, Any]]]: - group_key = None - group = [] - i = 0 - for row in iterator: - key = [row[k_i] for k_i in self._key_columns] - if group_key is None: - group_key = key - group.append(row) - elif group_key == key: - group.append(row) - else: - i += 1 - yield group - group = [row] - group_key = key - if group: - yield group - - def create_index(self): - key = None - delimiter = self._delimiter.encode("ascii") - with open_stream(self.filename, 'rb') as stream: - header = stream.readline() - header_cols = header.split(delimiter) - column_keys = ( - header_cols.index(b'ModifiedPeptide'), - header_cols.index(b'PrecursorCharge'), - ) - offset = stream.tell() - - line = stream.readline() - tokens = line.split(delimiter) - key = (tokens[column_keys[0]].strip(b"_"), tokens[column_keys[1]]) - n = 0 - self.index.add( - number=n, - offset=offset, - name=_ID_SEP.join(key).decode("utf8"), - analyte=None - ) - n += 1 - - # To hold previous values - last_offset = None - while line: - tokens = line.split(delimiter) - next_key = (tokens[column_keys[0]].strip(b"_"), tokens[column_keys[1]]) - if next_key != key: - key = next_key - self.index.add( - number=n, - offset=offset, - name=_ID_SEP.join(key).decode("utf8"), - analyte=None - ) - n += 1 - last_offset = stream.tell() - else: - offset = stream.tell() - line = stream.readline() - n += 1 - self.index.commit() - return n - - def _generate_peaks(self, batch: List[Dict[str, Any]]) -> List[Tuple[float, float, List[annotation.IonAnnotationBase], List]]: - peaks = [] - for row in batch: - mz = float(row['FragmentMz']) - intensity = float(row['RelativeIntensity']) - - series = row['FragmentType'] - ordinal = int(row['FragmentNumber']) - charge = int(row['FragmentCharge']) - - loss_type = row['FragmentLossType'] - if loss_type != NO_LOSS: - loss_type = ['-' + loss_type] - else: - loss_type = None - - annot = annotation.PeptideFragmentIonAnnotation( - series, ordinal, neutral_losses=loss_type, charge=charge, - mass_error=annotation.MassError(0, 'Da') - ) - - peak = [ - mz, intensity, [annot], [] - ] - peaks.append(peak) - return peaks - - def _build_analyte(self, description: Dict[str, Any], analyte: Analyte) -> Analyte: - pf_seq = _rewrite_modified_peptide_as_proforma(description['ModifiedPeptide']) - peptide = proforma.ProForma.parse(pf_seq) - analyte.add_attribute(STRIPPED_PEPTIDE_TERM, description['StrippedPeptide']) - analyte.add_attribute(PROFORMA_PEPTIDE_TERM, pf_seq) - analyte.add_attribute("MS:1001117|theoretical mass", peptide.mass) - analyte.add_attribute(CHARGE_STATE, int(description['PrecursorCharge'])) - - protein_group_id = analyte.get_next_group_identifier() - - - if 'UniProtIds' in description: - analyte.add_attribute( - "MS:1000885|protein accession", - description['UniProtIds'], - group_identifier=protein_group_id - ) - if 'Protein Name' in description: - analyte.add_attribute( - "MS:1000886|protein name", - description["Protein Name"], - group_identifier=protein_group_id - ) - if 'ProteinDescription' in description: - analyte.add_attribute( - "MS:1001088|protein description", - description['ProteinDescription'], - group_identifier=protein_group_id - ) - - if "OrganismId" in description: - analyte.add_attribute_group([ - ["MS:1001467|taxonomy: NCBI TaxID", f"NCBITaxon:{description['OrganismId']}|{description['Organisms']}"], - ["MS:1001469|taxonomy: scientific name", description['Organisms']], - ]) - - for key in self._custom_analyte_keys: - if key in description: - analyte.add_attribute_group([ - [CUSTOM_ATTRIBUTE_NAME, key], - [CUSTOM_ATTRIBUTE_VALUE, _parse_value(description[key])] - ]) - - return analyte - - def _parse_from_buffer(self, buffer: List[Dict[str, Any]], spectrum_index: int = None) -> Spectrum: - spec = self._new_spectrum() - descr = buffer[0] - - key = (descr['ModifiedPeptide'].strip("_"), descr['PrecursorCharge']) - - spec.add_attribute(SPECTRUM_NAME, ID_SEP.join(key)) - spec.add_attribute(SELECTED_ION_MZ, float(descr['PrecursorMz'])) - # Charge does not belong in the spectrum - # spec.add_attribute(CHARGE_STATE, int(descr['PrecursorCharge'])) - spec.add_attribute(SOURCE_FILE, urlify(descr['ReferenceRun'])) - spec.add_attribute(*self._spectrum_type()) - - spec.add_attribute_group([ - [CUSTOM_ATTRIBUTE_NAME, "LabeledPeptide"], - [CUSTOM_ATTRIBUTE_VALUE, descr['LabeledPeptide']] - ]) - - if 'IonMobility' in descr: - spec.add_attribute("MS:1002476|ion mobility drift time", float(descr['IonMobility'])) - if 'CV' in descr: - spec.add_attribute("MS:1001581|FAIMS compensation voltage", float(descr['CV'])) - if 'iRT' in descr: - spec.add_attribute("MS:1000896|normalized retention time", float(descr['iRT'])) - - analyte = self._new_analyte('1') - self._build_analyte(descr, analyte) - spec.add_analyte(analyte) - - for key in self._custom_spectrum_keys: - if key in descr: - spec.add_attribute_group([ - [CUSTOM_ATTRIBUTE_NAME, key], - [CUSTOM_ATTRIBUTE_VALUE, _parse_value(descr[key])] - ]) - - spec.peak_list = self._generate_peaks(buffer) - spec.add_attribute("MS:1003059|number of peaks", len(spec.peak_list)) - - if spectrum_index is not None: - spec.index = spectrum_index - else: - spec.index = -1 - spec.key = spec.index + 1 - return spec diff --git a/implementations/python/mzlib/backends/sptxt.py b/implementations/python/mzlib/backends/sptxt.py deleted file mode 100644 index 957f2a1..0000000 --- a/implementations/python/mzlib/backends/sptxt.py +++ /dev/null @@ -1,87 +0,0 @@ -import io -import re - -from typing import Dict, Tuple - -from mzlib.attributes import AttributeManager - -from mzlib.annotation import AnnotationStringParser - -from mzlib.backends.base import DEFAULT_VERSION, FORMAT_VERSION_TERM, LIBRARY_NAME_TERM -from mzlib.backends.utils import open_stream - -from .msp import MSPSpectralLibrary as _MSPSpectralLibrary -from .utils import CaseInsensitiveDict - - -annotation_pattern = re.compile(r"""^ -(?:(?:(?P[abyxcz]\.?)(?P\d+))| - (:?Int/(?P[ARNDCEQGHKMFPSTWYVILJarndceqghkmfpstwyvilj]+))| - (?Pp)| - (:?I(?P[ARNDCEQGHKMFPSTWYVIL])(?:(?PCAM)|[A-Z])?)| - (?:_(?P[^\s,/]+)) -) -(?P[+-]\d*(?:\.\d+)?) -(?:\^(?P[+-]?\d+))? -(?:\[M(?P(:?[+-]\d*[A-Z][A-Za-z0-9]*)+)\])? -(?:(?P\d*)i)? -(?:/(?P[+-]?\d+(?:\.\d+))(?Pppm)?)? -""", re.X) - - -class SPTXTAnnotationParser(AnnotationStringParser): - def __init__(self, pattern): - super().__init__(pattern) - - def _parse_string(self, annotation_string: str, **kwargs) -> Tuple[re.Match, Dict[str, str]]: - match, data = super()._parse_string(annotation_string, **kwargs) - if data['isotope'] is not None and not data['isotope']: - data['isotope'] = '1' - return match, data - - -parse_annotation = SPTXTAnnotationParser(annotation_pattern) - - -sptxt_spectrum_attribute_map = CaseInsensitiveDict({ - "TotalIonCurrent": "MS:1000285|total ion current", -}) - - -class SPTXTSpectralLibrary(_MSPSpectralLibrary): - file_format = "sptxt" - format_name = "sptxt" - - @classmethod - def guess_from_header(cls, filename: str) -> bool: - with open_stream(filename, 'r') as stream: - first_line = stream.readline() - i = 1 - while first_line.startswith("###") and i < 1000: - first_line = stream.readline() - i += 1 - if re.match("Name: ", first_line): - return True - if first_line.startswith("###"): - return True - return False - - def read_header(self) -> bool: - with open_stream(self.filename, 'r') as stream: - match, offset = self._parse_header_from_stream(stream) - return match - return False - - def _parse_header_from_stream(self, stream: io.IOBase) -> Tuple[bool, int]: - first_line = stream.readline() - attributes = AttributeManager() - attributes.add_attribute(FORMAT_VERSION_TERM, DEFAULT_VERSION) - attributes.add_attribute(LIBRARY_NAME_TERM, self.filename) - self.attributes.clear() - self.attributes._from_iterable(attributes) - if re.match("Name: ", first_line): - return True, 0 - return False, 0 - - def _parse_annotation(self, annotation: str, wrap_errors: bool = True, **kwargs): - return parse_annotation(annotation_string=annotation, wrap_errors=wrap_errors, **kwargs) diff --git a/implementations/python/mzlib/backends/text.py b/implementations/python/mzlib/backends/text.py deleted file mode 100644 index 9dd9b0d..0000000 --- a/implementations/python/mzlib/backends/text.py +++ /dev/null @@ -1,916 +0,0 @@ -import re -import os -import io -import logging -import warnings -import enum -import numbers - -from dataclasses import dataclass -from collections import deque -from typing import ClassVar, List, Optional, Tuple, Union, Iterable - -from mzlib.annotation import parse_annotation -from mzlib.spectrum import Spectrum -from mzlib.cluster import SpectrumCluster -from mzlib.attributes import Attribute, AttributeManager, Attributed, AttributeSet -from mzlib.analyte import Analyte, Interpretation, InterpretationMember -from mzlib.validate.object_rule import ValidationWarning - -from .base import ( - SpectralLibraryBackendBase, - _PlainTextSpectralLibraryBackendBase, - SpectralLibraryWriterBase, - FORMAT_VERSION_TERM, - AttributeSetTypes) -from .utils import try_cast, open_stream - -logger = logging.getLogger(__name__) -logger.addHandler(logging.NullHandler()) - - -term_pattern = re.compile( - r"^(?P(?P\S+:(?:\d|X)+)\|(?P[^=]+))") -key_value_term_pattern = re.compile( - r"^(?P(?P[A-Za-z0-9:.]+:(?:\d|X)+)\|(?P[^=]+?))\s*=\s*(?P.+)") -grouped_key_value_term_pattern = re.compile( - r"^\[(?P\d+)\](?P(?P\S+:(?:\d|X)+)\|(?P[^=]+?))\s*=\s*(?P.+)") -float_number = re.compile( - r"^\d+(.\d+)?") - - -class _SpectrumParserStateEnum(enum.Enum): - unknown = 0 - header = 1 - analyte = 2 - interpretation = 3 - interpretation_member = 4 - peaks = 5 - done = 6 - cluster = 7 - - -class _LibraryParserStateEnum(enum.Enum): - unknown = 0 - header = 1 - attribute_sets = 2 - content = 3 - - -ATTRIBUTE_SET_NAME = "MS:1003212|library attribute set name" -PEAK_ATTRIBUTE = "MS:1003254|peak attribute" - -START_OF_SPECTRUM_MARKER = re.compile(r"^<(?:Spectrum)(?:\s*=\s*(.+))?>") -START_OF_INTERPRETATION_MARKER = re.compile(r"^") -START_OF_ANALYTE_MARKER = re.compile(r"^") -START_OF_PEAKS_MARKER = re.compile(r"^") -START_OF_LIBRARY_MARKER = re.compile(r"^") -START_OF_INTERPRETATION_MEMBER_MARKER = re.compile(r"") -START_OF_ATTRIBUTE_SET = re.compile( - r"") -START_OF_CLUSTER = re.compile(r"") - -SPECTRUM_NAME_PRESENT = re.compile(r'MS:1003061\|(?:library )?spectrum name\s*=\s*') -SPECTRUM_NAME_MATCH = re.compile(r'MS:1003061\|(?:library )?spectrum name\s*=\s*(.+)') - -FALLBACK_PEAK_LINE_PATTERN = re.compile(r'(?P\d+(?:\.\d+)?)\s+(?P\d+(?:\.\d+)?)(?:\s+(?P.+))?') - -attribute_set_types = { - "spectrum": AttributeSetTypes.spectrum, - "analyte": AttributeSetTypes.analyte, - "interpretation": AttributeSetTypes.interpretation, - "cluster": AttributeSetTypes.cluster, -} - - -class _Scope: - state: _SpectrumParserStateEnum - attribute_group: Optional[str] - working_attribute_group: Optional[str] - - def __init__(self, state: _SpectrumParserStateEnum, attribute_group: Optional[str] = None, working_attribute_group: Optional[str] = None) -> None: - if working_attribute_group is None: - working_attribute_group = attribute_group - self.state = state - self.attribute_group = attribute_group - self.working_attribute_group = working_attribute_group - - def __repr__(self): - return f"{self.__class__.__name__}({self.state}, {self.attribute_group}, {self.working_attribute_group})" - - -class _EntryParser(_Scope): - """ - Moves the complexity and state management involved in parsing - a full entry out of :class:`TextSpectrumLibrary`, allowing it - to be factored into a bunch of helper methods around a single - piece of shared stated too granular for the main parser. - """ - - library: 'TextSpectralLibrary' - state: _SpectrumParserStateEnum - - spectrum: Optional[Spectrum] - cluster: Optional[SpectrumCluster] - analyte: Optional[Analyte] - interpretation: Optional[Interpretation] - interpretation_member: Optional[InterpretationMember] - attribute_group: Optional[str] - aggregation_types: List[str] - peak_list: List[Tuple] - - start_line_number: int - line_number: int = -1 - - def __init__(self, library, start_line_number: int, spectrum_index: Optional[int]) -> None: - super().__init__(_SpectrumParserStateEnum.header, None) - - self.library = library - self.start_line_number = start_line_number or 0 - self.spectrum_index = spectrum_index - - self.aggregation_types = None - self.peak_list = [] - - self.spectrum = None - self.cluster = None - self.analyte = None - self.interpretation = None - self.interpretation_member = None - - def _parse_attribute_into(self, line: str, store: Attributed, line_number_message: str): - self.library._parse_attribute_into(line, store, line_number_message, self) - - def real_line_number_or_nothing(self): - message = f" on line {self.line_number + self.start_line_number}" - if self.spectrum_index is not None: - message += f" in spectrum {self.spectrum_index}" - message += f" in state {self.state}" - return message - - def _parse_header(self, line): - if START_OF_SPECTRUM_MARKER.match(line): - self.state = _SpectrumParserStateEnum.header - self.spectrum = self.library._new_spectrum() - self.spectrum.index = self.spectrum_index - match = START_OF_SPECTRUM_MARKER.match(line) - self.spectrum.key = int(match.group(1)) or self.spectrum.index - 1 - return - - elif START_OF_PEAKS_MARKER.match(line): - self.state = _SpectrumParserStateEnum.peaks - return - - elif START_OF_INTERPRETATION_MARKER.match(line): - self.state = _SpectrumParserStateEnum.interpretation - match = START_OF_INTERPRETATION_MARKER.match(line) - if self.interpretation is not None: - self.spectrum.add_interpretation(self.interpretation) - self.interpretation = self.library._new_interpretation(match.group(1)) - self.spectrum.add_interpretation(self.interpretation) - self.analyte = None - return - - elif START_OF_ANALYTE_MARKER.match(line): - self.state = _SpectrumParserStateEnum.analyte - match = START_OF_ANALYTE_MARKER.match(line) - self.analyte = self.library._new_analyte(match.group(1)) - self.spectrum.add_analyte(self.analyte) - return - - elif START_OF_CLUSTER.match(line): - self.state = _SpectrumParserStateEnum.cluster - self.cluster = self.library._new_cluster() - match = START_OF_CLUSTER.match(line) - self.cluster.key = int(match.group(1)) or self.cluster.index - 1 - return - - self._parse_attribute_into( - line, self.spectrum, self.real_line_number_or_nothing) - - def _parse_interpretation(self, line): - if START_OF_ANALYTE_MARKER.match(line): - warnings.warn( - f"An analyte found after an interpretation was encountered, {self.real_line_number_or_nothing()}") - self.state = _SpectrumParserStateEnum.analyte - match = START_OF_ANALYTE_MARKER.match(line) - if self.analyte is not None: - self.spectrum.add_analyte(self.analyte) - self.analyte = self.library._new_analyte(match.group(1)) - self.spectrum.add_analyte(self.analyte) - return - elif START_OF_INTERPRETATION_MARKER.match(line): - self.state = _SpectrumParserStateEnum.interpretation - match = START_OF_INTERPRETATION_MARKER.match(line) - if self.interpretation is not None: - self.spectrum.add_interpretation(self.interpretation) - self.interpretation = self.library._new_interpretation(match.group(1)) - self.spectrum.add_interpretation(self.interpretation) - self.analyte = None - return - elif START_OF_PEAKS_MARKER.match(line): - self.state = _SpectrumParserStateEnum.peaks - return - elif START_OF_INTERPRETATION_MEMBER_MARKER.match(line): - self.state = _SpectrumParserStateEnum.interpretation_member - match = START_OF_INTERPRETATION_MEMBER_MARKER.match(line) - - if self.interpretation_member is not None: - self.interpretation.add_member_interpretation(self.interpretation_member) - - self.interpretation_member = InterpretationMember(match.group(1)) - self.interpretation.add_member_interpretation(self.interpretation_member) - return - - self._parse_attribute_into( - line, self.interpretation.attributes, self.real_line_number_or_nothing) - self.library._analyte_interpretation_link(self.spectrum, self.interpretation) - - def _parse_interpretation_member(self, line): - if START_OF_PEAKS_MARKER.match(line): - self.state = _SpectrumParserStateEnum.peaks - self.interpretation_member = None - self.interpretation = None - return - elif START_OF_INTERPRETATION_MARKER.match(line): - self.state = _SpectrumParserStateEnum.interpretation - match = START_OF_INTERPRETATION_MARKER.match(line) - if self.interpretation is not None: - self.spectrum.add_interpretation(self.interpretation) - self.interpretation = self.library._new_interpretation(match.group(1)) - self.spectrum.add_interpretation(self.interpretation) - self.interpretation_member = None - return - elif START_OF_INTERPRETATION_MEMBER_MARKER.match(line): - self.state = _SpectrumParserStateEnum.interpretation_member - match = START_OF_INTERPRETATION_MEMBER_MARKER.match(line) - if self.interpretation_member is not None: - self.interpretation.add_member_interpretation(self.interpretation_member) - self.interpretation_member = InterpretationMember(match.group(1)) - self.interpretation.add_member_interpretation(self.interpretation_member) - return - - self._parse_attribute_into( - line, self.interpretation_member, self.real_line_number_or_nothing) - - def _parse_analyte(self, line): - if START_OF_PEAKS_MARKER.match(line): - self.state = _SpectrumParserStateEnum.peaks - if self.analyte is not None: - self.spectrum.add_analyte(self.analyte) - self.analyte = None - return - - elif START_OF_ANALYTE_MARKER.match(line): - self.state = _SpectrumParserStateEnum.analyte - match = START_OF_ANALYTE_MARKER.match(line) - if self.analyte is not None: - self.spectrum.add_analyte(self.analyte) - self.analyte = self.library._new_analyte(match.group(1)) - return - - elif START_OF_INTERPRETATION_MARKER.match(line): - self.state = _SpectrumParserStateEnum.interpretation - match = START_OF_INTERPRETATION_MARKER.match(line) - if self.analyte is not None: - self.spectrum.add_analyte(self.analyte) - self.analyte = None - - # Somehow we have an in-progress Interpretation that hasn't been cleared yet. - # This should probably be an error strictly speaking. - if self.interpretation is not None: - warnings.warn( - f"Interleaved analytes and interpretations detected at {self.real_line_number_or_nothing()}") - self.spectrum.add_interpretation(self.interpretation) - self.interpretation = self.library._new_interpretation(match.group(1)) - self.spectrum.add_interpretation(self.interpretation) - return - - self._parse_attribute_into(line, self.analyte, self.real_line_number_or_nothing) - - def _parse_peaks(self, line): - # TODO: When we know more about how different aggregations are formatted, - # look that up here once so we remember it and can use it to process the - # aggregation columns - if self.aggregation_types is None: - self.aggregation_types = self.spectrum.peak_aggregations - match = float_number.match(line) - if match is not None: - tokens = line.split("\t") - n_tokens = len(tokens) - if n_tokens == 1 and ' ' in line: - if match := FALLBACK_PEAK_LINE_PATTERN.match(line): - tokens = match.groups() - n_tokens = len(tokens) - warnings.warn( - f"Space character delimiter found in peak line{self.real_line_number_or_nothing()}", - ValidationWarning - ) - if n_tokens == 2: - mz, intensity = tokens - annotation = parse_annotation("?") - self.peak_list.append([float(mz), float(intensity), annotation, []]) - elif n_tokens == 3: - mz, intensity, annotation = tokens - if not annotation: - annotation = "?" - annotation = parse_annotation(annotation, wrap_errors=True) - self.peak_list.append([float(mz), float(intensity), annotation, []]) - elif n_tokens > 3: - mz, intensity, annotation, *aggregation = tokens - if not annotation: - annotation = "?" - annotation = parse_annotation(annotation, wrap_errors=True) - self.peak_list.append( - [float(mz), float(intensity), annotation, [try_cast(agg) for agg in aggregation]]) - else: - raise ValueError( - f"Malformed peak line {line} with {n_tokens} entries{self.real_line_number_or_nothing()}") - else: - raise ValueError(f"Malformed peak line {line}{self.real_line_number_or_nothing()}") - - def _parse_cluster(self, line): - if START_OF_SPECTRUM_MARKER.match(line): - raise ValueError( - f"Clusters should not include spectrum sections {self.real_line_number_or_nothing()}") - - elif START_OF_PEAKS_MARKER.match(line): - raise ValueError( - f"Clusters should not include peaks {self.real_line_number_or_nothing()}") - - elif START_OF_INTERPRETATION_MARKER.match(line): - raise ValueError( - f"Clusters should not include interpretation sections {self.real_line_number_or_nothing()}") - - elif START_OF_ANALYTE_MARKER.match(line): - raise ValueError( - f"Clusters should not include analyte sections {self.real_line_number_or_nothing()}") - - elif START_OF_INTERPRETATION_MEMBER_MARKER.match(line): - raise ValueError( - f"Clusters should not include interpretation member sections {self.real_line_number_or_nothing()}") - - self._parse_attribute_into( - line, self.cluster, self.real_line_number_or_nothing) - - def parse(self, buffer: Iterable[str]): - line: str - for line_number, line in enumerate(buffer): - self.line_number = line_number - line = line.strip() - if not line: - break - # Skip comments for now, no round-trip - if line.startswith("#"): - continue - elif self.state == _SpectrumParserStateEnum.header: - self._parse_header(line) - elif self.state == _SpectrumParserStateEnum.interpretation: - self._parse_interpretation(line) - elif self.state == _SpectrumParserStateEnum.interpretation_member: - self._parse_interpretation_member(line) - elif self.state == _SpectrumParserStateEnum.analyte: - self._parse_analyte(line) - elif self.state == _SpectrumParserStateEnum.peaks: - self._parse_peaks(line) - elif self.state == _SpectrumParserStateEnum.cluster: - self._parse_cluster(line) - else: - raise ValueError( - f"Unknown state {self.state}{self.real_line_number_or_nothing()}") - if self.cluster: - return self.cluster - self.spectrum.peak_list = self.peak_list - # Backfill analytes into interpretations that never explicitly listed them. - self.library._default_interpretation_to_analytes(self.spectrum) - return self.spectrum - - -def _is_header_line(line: Union[str, bytes]) -> bool: - if isinstance(line, bytes): - line = line.decode('utf8') - if START_OF_SPECTRUM_MARKER.match(line): - return False - if START_OF_CLUSTER.match(line): - return False - if SPECTRUM_NAME_PRESENT.match(line): - return False - return True - - -class TextSpectralLibrary(_PlainTextSpectralLibraryBackendBase): - """ - A reader for the plain text serialization of the mzSpecLib spectral library foramt. - - This implementation may operate on a stream opened in binary mode or a file path. - If using a non-seekable stream, the random access or search methods may not be - supported. - """ - - file_format: ClassVar[List[str]] = ["mzlb.txt", "mzlib.txt"] - format_name: ClassVar[str] = "text" - - @classmethod - def guess_from_header(cls, filename: str) -> bool: - with open_stream(filename, 'r', encoding='utf8') as stream: - first_line = stream.readline() - if (START_OF_SPECTRUM_MARKER.match(first_line) or - START_OF_LIBRARY_MARKER.match(first_line) or - START_OF_CLUSTER.match(first_line)): - return True - return False - - def _parse_header_from_stream(self, stream: io.RawIOBase) -> Tuple[bool, int]: - nbytes = 0 - first_line = stream.readline() - nbytes += len(first_line) - first_line = first_line.decode('utf8') - - state = _LibraryParserStateEnum.unknown - - current_attribute_set = None - current_attribute_set_type = None - - if not _is_header_line(first_line): - return True, 0 - elif START_OF_LIBRARY_MARKER.match(first_line): - state = _LibraryParserStateEnum.header - match = START_OF_LIBRARY_MARKER.match(first_line) - version = match.group(1) - attributes = AttributeManager() - attributes.add_attribute(FORMAT_VERSION_TERM, version) - line = stream.readline() - while _is_header_line(line): - nbytes += len(line) - line = line.strip().decode('utf8') - if not line: - line = stream.readline() - continue - match = START_OF_ATTRIBUTE_SET.match(line) - if match: - state = _LibraryParserStateEnum.attribute_sets - if current_attribute_set is not None: - self._add_attribute_set( - current_attribute_set, current_attribute_set_type) - - current_attribute_set_type = attribute_set_types[ - match.group(1).lower()] - attrib_set_name = match.group(2) - current_attribute_set = AttributeSet(attrib_set_name, []) - else: - match = key_value_term_pattern.match(line) - - # We found a single attribute - if match is not None: - d = match.groupdict() - # If we're in an attribute set, store it in the attribute set - if state == _LibraryParserStateEnum.attribute_sets: - current_attribute_set.add_attribute( - d['term'], try_cast(d['value'])) - else: # Otherwise store it in the library level attributes - attributes.add_attribute( - d['term'], try_cast(d['value'])) - - line = stream.readline() - # nbytes += len(line) - continue - - if line.startswith("["): - # We found a grouped attribute - match = grouped_key_value_term_pattern.match(line) - if match is not None: - d = match.groupdict() - # If we're in an attribute set, store it in the attribute - # set - if state == _LibraryParserStateEnum.attribute_sets: - current_attribute_set.add_attribute( - d['term'], try_cast(d['value']), d['group_id']) - current_attribute_set.group_counter = int(d['group_id']) - else: # Otherwise store it in the library level attributes - attributes.add_attribute( - d['term'], try_cast(d['value']), d['group_id']) - attributes.group_counter = int(d['group_id']) - - line = stream.readline() - # nbytes += len(line) - continue - else: - raise ValueError( - f"Malformed grouped attribute {line}") - elif "=" in line: - name, value = line.split("=", 1) - if state == _LibraryParserStateEnum.attribute_sets: - current_attribute_set.add_attribute(name, value) - else: - attributes.add_attribute(name, value) - else: - raise ValueError(f"Malformed attribute line {line}") - line = stream.readline() - - if current_attribute_set is not None: - self._add_attribute_set( - current_attribute_set, current_attribute_set_type) - self.attributes.clear() - self.attributes._from_iterable(attributes) - print(f"Header contained {nbytes} bytes") - return True, nbytes - return False, 0 - - def read_header(self) -> bool: - if isinstance(self.filename, io.IOBase): - return self._parse_header_from_stream(self.filename)[0] - with open_stream(self.filename, 'rb') as stream: - return self._parse_header_from_stream(stream)[0] - - def create_index(self) -> int: - """ - Populate the spectrum index - - Returns - ------- - n_spectra: int - The number of entries read - """ - #### Check that the spectrum library filename isvalid - filename = self.filename - - #### Determine the filesize - file_size = os.path.getsize(filename) - - with open_stream(filename, 'rt', encoding='utf8') as infile: - state = 'header' - entry_buffer = deque() - - n_spectra = 0 - n_clusters = 0 - - start_index = 0 - file_offset = 0 - - line_beginning_file_offset = 0 - spectrum_file_offset = 0 - spectrum_name = '' - current_key = None - entry_is_cluster = False - - # Required for counting file_offset manually (LF vs CRLF) - infile.readline() - file_offset_line_ending = len(infile.newlines) - 1 - infile.seek(0) - - logger.debug(f"Reading {filename} ({file_size} bytes)...") - while 1: - line = infile.readline() - if len(line) == 0: - break - - line_beginning_file_offset = file_offset - - #### tell() is twice as slow as counting it myself - file_offset += len(line) + file_offset_line_ending - - line = line.rstrip() - if state == 'header': - - if is_spec := START_OF_SPECTRUM_MARKER.match(line): - current_key = int(is_spec.group(1)) - state = 'body' - spectrum_file_offset = line_beginning_file_offset - entry_is_cluster = False - elif is_clus := START_OF_CLUSTER.match(line): - current_key = int(is_clus.group(1)) - state = 'body' - spectrum_file_offset = line_beginning_file_offset - entry_is_cluster = True - else: - continue - - if state == 'body': - if len(line) == 0: - continue - - is_spec = START_OF_SPECTRUM_MARKER.match(line) - is_clus = START_OF_CLUSTER.match(line) - if (is_spec) or (is_clus): - if len(entry_buffer) > 0: - if not entry_is_cluster: - if not spectrum_name: - raise ValueError("No spectrum name") - self.index.add( - number=current_key, - offset=spectrum_file_offset, - name=spectrum_name, - analyte=None) - n_spectra += 1 - current_key = int(is_spec.group(1)) if is_spec else int(is_clus.group(1)) - #### Commit every now and then - if n_spectra % 10000 == 0: - self.index.commit() - logger.info( - f"Processed {file_offset} bytes, {n_spectra} spectra read, {n_clusters} clusters read") - else: - self.index.add_cluster(number=current_key, offset=spectrum_file_offset) - if n_clusters % 10000 == 0: - self.index.commit() - logger.info( - f"Processed {file_offset} bytes, {n_spectra} spectra read, {n_clusters} clusters read") - n_clusters += 1 - current_key = int(is_spec.group(1)) if is_spec else int(is_clus.group(1)) - - entry_buffer.clear() - entry_is_cluster = bool(is_clus) - spectrum_file_offset = line_beginning_file_offset - spectrum_name = '' - - if SPECTRUM_NAME_PRESENT.match(line): - if match := SPECTRUM_NAME_MATCH.match(line): - spectrum_name = match.group(1) - - entry_buffer.append(line) - - - if spectrum_name: - self.index.add( - number=current_key, - offset=spectrum_file_offset, - name=spectrum_name, - analyte=None) - self.index.commit() - n_spectra += 1 - logger.info( - f"Processed {file_offset} bytes, {n_spectra} spectra read, {n_clusters} clusters read") - elif entry_is_cluster: - self.index.add_cluster( - number=current_key, - offset=spectrum_file_offset, - ) - self.index.commit() - n_clusters += 1 - logger.info( - f"Processed {file_offset} bytes, {n_spectra} spectra read, {n_clusters} clusters read") - - #### Flush the index - self.index.commit() - - return n_spectra - - def _buffer_from_stream(self, infile: Iterable[str]) -> List: - state = 'body' - spectrum_buffer = [] - - for line in infile: - line = line.rstrip() - if state == 'body': - if len(line) == 0: - continue - if START_OF_SPECTRUM_MARKER.match(line) or START_OF_CLUSTER.match(line): - if len(spectrum_buffer) > 0: - return spectrum_buffer - spectrum_buffer.append(line) - return spectrum_buffer - - def _prepare_attribute_dict(self, match): - key = match['term_accession'] - value = match['value'] - try: - term = self.find_term_for(key) - match['value'] = term.value_type(value) - except KeyError: - match['value'] = try_cast(value) - - def _parse_attribute(self, line: str, line_number_message=lambda: '', scope: Optional[_Scope]=None) -> Union[Attribute, AttributeSet]: - match = key_value_term_pattern.match(line) - if scope is None: - scope = _Scope(None, None) - if match is not None: - d = match.groupdict() - self._prepare_attribute_dict(d) - if d['term'] == ATTRIBUTE_SET_NAME: - if _SpectrumParserStateEnum.header == scope.state: - attr_set = self.spectrum_attribute_sets[d['value']] - elif _SpectrumParserStateEnum.analyte == scope.state: - attr_set = self.analyte_attribute_sets[d['value']] - elif _SpectrumParserStateEnum.interpretation == scope.state: - attr_set = self.interpretation_attribute_sets[d['value']] - elif _SpectrumParserStateEnum.cluster == scope.state: - attr_set = self.cluster_attribute_sets[d['value']] - else: - raise ValueError(f"Cannot define attribute sets for {scope.state}") - return attr_set - attr = Attribute(d["term"], try_cast(d["value"])) - return attr - elif line.startswith("["): - match = grouped_key_value_term_pattern.match(line) - if match is not None: - d = match.groupdict() - self._prepare_attribute_dict(d) - attr = Attribute(d['term'], try_cast(d['value']), d['group_id']) - return attr - else: - raise ValueError(f"Malformed grouped attribute {line}{line_number_message()}") - elif "=" in line: - name, value = line.split("=", 1) - attr = Attribute(name, try_cast(value)) - return attr - else: - raise ValueError(f"Malformed attribute line {line}{line_number_message()}") - - def _parse_attribute_into(self, line: str, store: Attributed, - line_number_message=lambda:'', - scope: Optional[_Scope]=None) -> bool: - if scope is None: - scope = _Scope(None, None) - attr = self._parse_attribute(line, line_number_message, scope) - if isinstance(attr, AttributeSet): - attr.apply(store) - else: - if attr.group_id: - if attr.group_id != scope.attribute_group: - scope.attribute_group = attr.group_id - scope.working_attribute_group = store.get_next_group_identifier() - attr.group_id = scope.working_attribute_group - else: - attr.group_id = scope.working_attribute_group - store.add_attribute(attr.key, attr.value, attr.group_id) - return True - - def _parse(self, buffer: Iterable[str], spectrum_index: int = None, - start_line_number: int=None) -> Union[Spectrum, SpectrumCluster]: - parser = _EntryParser(self, start_line_number, spectrum_index) - return parser.parse(buffer) - - def get_spectrum(self, spectrum_number: int=None, - spectrum_name: str=None) -> Spectrum: - # keep the two branches separate for the possibility that this is not - # possible with all index schemes. - if spectrum_number is not None: - if spectrum_name is not None: - raise ValueError( - "Provide only one of spectrum_number or spectrum_name") - index_record = self.index.record_for(spectrum_number) - offset = index_record.offset - elif spectrum_name is not None: - index_record = self.index.record_for(spectrum_name) - offset = index_record.offset - spectrum_number = index_record.number - else: - raise ValueError("Must provide either spectrum_number or spectrum_name argument") - - buffer = self._get_lines_for(offset) - spectrum = self._parse(buffer, index_record.index) - return spectrum - - def get_cluster(self, cluster_number: int) -> SpectrumCluster: - offset = self.index.offset_for_cluster(cluster_number) - buffer = self._get_lines_for(offset) - cluster = self._parse(buffer, cluster_number) - return cluster - - -class TextSpectralLibraryWriter(SpectralLibraryWriterBase): - """ - Write a spectral library to the plain text serialization of the mzSpecLib spectral library format. - - Attributes - ---------- - version : str - The format version to write in semver-compatible notation - compact_interpretation : bool, default :const:`True` - Whether to elect to write compact interpretation member sections when there is only - one interpretation and only one interpretation member by inlining the interpretation - member attributes into the interpretation. Both forms are valid, one is just less - verbose. - """ - - file_format = "mzlb.txt" - format_name = "text" - default_version = '1.0' - - def __init__(self, filename, version=None, compact_interpretations: bool=True, **kwargs): - super(TextSpectralLibraryWriter, self).__init__(filename) - self.version = version - self._coerce_handle(self.filename) - self.compact_interpretations = compact_interpretations - - def _write_attributes(self, attributes: Attributed): - for attribute in attributes: - value = attribute.value - if ":" in attribute.key: - try: - term = self.find_term_for(attribute.key.split("|")[0]) - value = term.value_type.format(value) - except (KeyError, ValueError): - pass - if attribute.group_id is None: - self.handle.write(f"{attribute.key}={value}\n") - else: - self.handle.write( - f"[{attribute.group_id}]{attribute.key}={value}\n") - - def write_header(self, library: SpectralLibraryBackendBase): - if self.version is None: - version = library.attributes.get_by_name("format version") - if version is None: - version = self.default_version - else: - version = self.version - self.handle.write("\n" % (version, )) - self._write_attributes(library.attributes) - for attr_set in library.spectrum_attribute_sets.values(): - self.write_attribute_set(attr_set, AttributeSetTypes.spectrum) - - for attr_set in library.analyte_attribute_sets.values(): - self.write_attribute_set(attr_set, AttributeSetTypes.analyte) - - for attr_set in library.interpretation_attribute_sets.values(): - self.write_attribute_set(attr_set, AttributeSetTypes.interpretation) - - def write_attribute_set(self, attribute_set: AttributeSet, - attribute_set_type: AttributeSetTypes): - if attribute_set_type == AttributeSetTypes.spectrum: - set_type = "Spectrum" - elif attribute_set_type == AttributeSetTypes.analyte: - set_type = "Analyte" - elif attribute_set_type == AttributeSetTypes.interpretation: - set_type = "Interpretation" - elif attribute_set_type == AttributeSetTypes.cluster: - set_type = "Cluster" - - header = f"\n" - self.handle.write(header) - self._write_attributes(attribute_set.attributes) - if attribute_set.attributes: - self.handle.write('\n') - - def write_spectrum(self, spectrum: Spectrum): - self.handle.write(f"\n") - attribs_of = list(self._filter_attributes( - spectrum, - self._not_entry_key_or_index) - ) - self._write_attributes(attribs_of) - for analyte in spectrum.analytes.values(): - self.handle.write(f"\n") - self._write_attributes(analyte.attributes) - _n_interps = len(spectrum.interpretations) - for interpretation in spectrum.interpretations.values(): - interpretation: Interpretation - - if len(spectrum.analytes) == 1: - attribs_of = list(self._filter_attributes( - interpretation, self._not_analyte_mixture_term)) - else: - attribs_of = interpretation.attributes - - self.handle.write(f"\n") - self._write_attributes(attribs_of) - - # When there is only one interpretation and only one interpretation member - # interpretation member attributes are written out as part of the interpretation - # itself. - if _n_interps == 1 and len(interpretation.member_interpretations) == 1 and self.compact_interpretations: - for member in interpretation.member_interpretations.values(): - self._write_attributes(member.attributes) - else: - for member in interpretation.member_interpretations.values(): - member: InterpretationMember - self.handle.write(f"\n") - self._write_attributes(member.attributes) - self.handle.write("\n") - for peak in spectrum.peak_list: - peak_parts = [ - str(peak[0]), - str(peak[1]), - '?' if not peak[2] else ",".join(map(str, peak[2])) - ] - if peak[3]: - peak_parts.append('\t'.join(map(format_aggregation, peak[3]))) - self.handle.write("\t".join(peak_parts) + "\n") - self.handle.write("\n") - - def write_cluster(self, cluster: SpectrumCluster): - self.handle.write(f"\n") - attribs_of = list(self._filter_attributes( - cluster, - self._not_entry_key_or_index) - ) - self._write_attributes(attribs_of) - self.handle.write("\n") - - def close(self): - self.handle.close() - - -def format_aggregation(value: Union[numbers.Number, str]) -> str: - if isinstance(value, numbers.Number): - return "%0.4g" % value - else: - return value - - -def format_spectrum(spectrum: Spectrum, **kwargs) -> str: - buffer = io.StringIO() - writer = TextSpectralLibraryWriter(buffer, **kwargs) - writer.write_spectrum(spectrum) - return buffer.getvalue() - diff --git a/implementations/python/mzlib/backends/utils.py b/implementations/python/mzlib/backends/utils.py deleted file mode 100644 index 0985e4c..0000000 --- a/implementations/python/mzlib/backends/utils.py +++ /dev/null @@ -1,208 +0,0 @@ -import os -import io -import gzip - -from collections import deque -from urllib import parse as urlparse -from typing import Any, Dict, Iterable, Mapping, Optional, Union - -DEFAULT_BUFFER_SIZE = int(2e6) -GZIP_MAGIC = b'\037\213' - -GzipFile = gzip.GzipFile - -try: - # Fast random acces with Gzip compatibility - import idzip - idzip.compressor.IdzipWriter.enforce_extension = False - - GzipFile = idzip.IdzipFile -except ImportError: - pass - - -class _LineBuffer(object): - """ - An implementation detail that treats a stream/iterator over line strings as LIFO - queue that can have lines pushed back onto it. - """ - - lines: deque - stream: io.IOBase - last_line: str - encoding: Optional[str] - _stream_is_file_like: bool - - def __init__(self, stream: io.IOBase, lines: Iterable=None, last_line: str=None, encoding: Optional[str]=None): - if lines is None: - lines = [] - self.lines = deque(lines) - self.stream = stream - self.last_line = last_line - self.encoding = encoding - self._stream_is_file_like = hasattr(self.stream, 'readline') - - def readline(self) -> Union[bytes, str]: - if self.lines: - line = self.lines.popleft() - else: - line = self.stream.readline() if self._stream_is_file_like else next(self.stream) - self.last_line = line - if self.encoding: - return line.decode(self.encoding) - return line - - def push_line(self, line=None): - if line is None: - line = self.last_line - self.last_line = None - if line is None: - raise ValueError("Cannot push empty value after the backtrack line is consumed") - self.lines.appendleft(line) - - def __iter__(self): - while self.lines: - line = self.lines.popleft() - self.last_line = line - if self.encoding: - yield line.decode(self.encoding) - else: - yield line - for line in self.stream: - self.last_line = line - if self.encoding: - yield line.decode(self.encoding) - else: - yield line - - def __getattr__(self, attr): - return getattr(self.stream, attr) - - -def try_cast(value: Any) -> Union[str, int, float, Any]: - """ - Given a value, if it is a string, attempt to convert it to a numeric type, - or else return it as is. - """ - if value is None: - return value - if not isinstance(value, str): - return value - try: - return int(value) - except ValueError: - pass - try: - return float(value) - except ValueError: - pass - return value - - -def test_gzipped(f) -> bool: - """ - Checks the first two bytes of the - passed file for gzip magic numbers - - Parameters - ---------- - f : file-like or path-like - The file to test - - Returns - ------- - bool - """ - if isinstance(f, os.PathLike): - f = io.open(f, 'rb') - try: - current = f.tell() - except OSError: - return False - f.seek(0) - magic = f.read(2) - f.seek(current) - return magic == GZIP_MAGIC - - -def starts_with_gz_magic(bytestring): - """ - Test whether or not a byte string starts with - the GZIP magic bytes. - - Parameters - ---------- - bytestring : bytes - The bytes to test. - - Returns - ------- - bool - """ - return bytestring.startswith(GZIP_MAGIC) - - -def open_stream(f: Union[io.IOBase, os.PathLike], mode='rt', buffer_size: Optional[int]=None, encoding: Optional[str]='utf8', newline=None): - """ - Select the file reading type for the given path or stream. - - Detects whether the file is gzip encoded. - """ - if buffer_size is None: - buffer_size = DEFAULT_BUFFER_SIZE - if 'r' in mode: - if not hasattr(f, 'read'): - f = io.open(f, 'rb') - if not isinstance(f, io.BufferedReader) and not isinstance(f, io.TextIOWrapper): - buffered_reader = io.BufferedReader(f, buffer_size) - else: - buffered_reader = f - if test_gzipped(buffered_reader): - handle = GzipFile(fileobj=buffered_reader, mode='rb') - else: - handle = buffered_reader - else: - raise NotImplementedError("Haven't implemented automatic output stream determination") - try: - fmode = f.mode - except AttributeError: - fmode = 'b' - if "b" not in mode and "b" in fmode: - handle = io.TextIOWrapper(handle, encoding=encoding, newline=newline) - return handle - - -class CaseInsensitiveDict(Dict[str, Any]): - """A case sensitive version of a dictionary with string keys.""" - - def __init__(self, base=None, **kwargs): - if base is not None: - self.update(base) - if kwargs: - self.update(kwargs) - - def __getitem__(self, key: str): - return super().__getitem__(key.lower()) - - def __setitem__(self, key: str, value): - super().__setitem__(key.lower(), value) - - def __delitem__(self, key: str): - super().__delitem__(key.lower()) - - def __contains__(self, __o: str) -> bool: - return super().__contains__(__o.lower()) - - def get(self, key: str, default=None): - return super().get(key.lower(), default) - - def update(self, value: Mapping[str, Any]): - super().update({k.lower(): v for k, v in value.items()}) - - -def urlify(path: str) -> str: - """Convert a path into a URL if it is not already one.""" - parsed = urlparse.urlparse(path) - if parsed.scheme == '': - parsed = parsed._replace(scheme='file') - return urlparse.urlunparse(parsed) \ No newline at end of file diff --git a/implementations/python/mzlib/cluster.py b/implementations/python/mzlib/cluster.py deleted file mode 100644 index 7bba278..0000000 --- a/implementations/python/mzlib/cluster.py +++ /dev/null @@ -1,57 +0,0 @@ -from __future__ import print_function - -from dataclasses import dataclass - -from typing import Dict, List - -from mzlib.attributes import AttributeManager, AttributeManagedProperty, AttributeGroupFacet -from .utils import ensure_iter, flatten - -SIMILAR_SPECTRUM_KEYS = "MS:1003263|similar spectrum keys" -SIMILAR_SPECTRUM_USI = "MS:1003264|similar spectrum USI" - -CLUSTER_KEY = "MS:1003267|spectrum cluster key" -CLUSTER_SIZE = "MS:1003320|spectrum cluster size" - -CLUSTER_MEMBERS_KEYS = "MS:1003268|spectrum cluster member spectrum keys" -CLUSTER_MEMBER_USI = "MS:1003269|spectrum cluster member USI" - -CLUSTER_SUMMARY_STATS = "MS:1003321|summary statistics of clustered spectra" - - -@dataclass -class ClusterMemberRef: - pass - - -@dataclass -class SpectrumRef(ClusterMemberRef): - key: str - - -@dataclass -class USIRef(ClusterMemberRef): - usi: str - - @property - def key(self) -> str: - return self.usi - - -class SpectrumCluster(AttributeManager): - def __init__(self, attributes: List=None): - super().__init__(attributes) - - key = AttributeManagedProperty[int](CLUSTER_KEY) - _member_references = AttributeManagedProperty(CLUSTER_MEMBERS_KEYS) - _cluster_member_usis = AttributeManagedProperty(CLUSTER_MEMBER_USI) - - size = AttributeManagedProperty[int](CLUSTER_SIZE) - - @property - def members(self) -> List[ClusterMemberRef]: - internal_refs = [ - SpectrumRef(k) for k in flatten(ensure_iter(self._member_references)) - ] - usi_members = [USIRef(k) for k in ensure_iter(self._cluster_member_usis)] - return internal_refs + usi_members diff --git a/implementations/python/mzlib/defaults.py b/implementations/python/mzlib/defaults.py deleted file mode 100644 index 386fb5b..0000000 --- a/implementations/python/mzlib/defaults.py +++ /dev/null @@ -1,5 +0,0 @@ - -DEFAULT_UNITS = { - "MS:1000224": "UO:0000002|mass", - "MS:1000744": "MS:1000040|m/z" -} diff --git a/implementations/python/mzlib/draw.py b/implementations/python/mzlib/draw.py deleted file mode 100644 index 0d98907..0000000 --- a/implementations/python/mzlib/draw.py +++ /dev/null @@ -1,178 +0,0 @@ -from collections import defaultdict - -from matplotlib import pyplot as plt -from matplotlib import patheffects as path_effects - -import numpy as np - -from .annotation import InvalidAnnotation, Unannotated - - -series_to_color = { - 'b': 'crimson', - 'y': 'steelblue', - 'a': 'darkorange', - 'c': 'violet', - 'z': 'dodgerblue', - 'internal': 'purple', - 'precursor': 'goldenrod', - 'immonium': 'maroon', - 'reporter': 'skyblue', - 'external': 'grey', - 'formula': 'forestgreen' -} - - -def peaklist_to_vector(peaklist, width=0.000001): - """Convert a list of discrete centroided peaks into a pair of continuous m/z - and intensity arrays - Parameters - ---------- - peaklist : :class:`~Iterable` of :class:`~.PeakLike` - The collection of peaks to convert - width : float, optional - The spacing between the center of the peak and it's shoulders - Returns - ------- - np.ndarray: - The generated m/z array - np.ndarray: - The generated intensity array - Raises - ------ - TypeError - When the input could not be coerced into a peak list - """ - mzs = [] - intensities = [] - for peak in sorted(peaklist, key=lambda x: x[0]): - mzs.append(peak[0] - width) - intensities.append(0.) - mzs.append(peak[0]) - intensities.append(peak[1]) - mzs.append(peak[0] + width) - intensities.append(0.) - return np.array(mzs), np.array(intensities) - - -def draw_spectrum(spectrum, ax=None, normalize=False, label_threshold=0.1, label_rotation=0, **kwargs): - """ - Draw and annotate a Spectrum. - - Parameters - ---------- - spectrum: :class:`~.Spectrum` - The annotated spectrum to draw. - ax : matplotlib.Axes, optional - The axis to draw the plot on. If missing, a new one will be created using - :func:`matplotlib.pyplot.subplots` - normalize: bool, optional - if `True`, will normalize the abundance dimension to be between 0 and 100% - pretty: bool, optional - If `True`, will call :func:`_beautify_axes` on `ax` - label_threshold: float, optional - The minimum intensity to label a peak for - label_rotation : float, optional - The degrees of rotation to apply to peak labels - **kwargs - Passed to :meth:`matplotlib.Axes.plot` - Returns - ------- - matplotlib.Axes - """ - pretty = kwargs.pop("pretty", True) - if ax is None: - _, ax = plt.subplots(1) - mz_array, intensity_array = peaklist_to_vector(spectrum.peak_list) - unscaled_max = intensity_array.max() - - if normalize: - intensity_array = intensity_array / intensity_array.max() * 100.0 - - kwargs.setdefault("color", 'black') - kwargs.setdefault("lw", 0.75) - ax.plot(mz_array, intensity_array, **kwargs) - - max_intensity = intensity_array.max() - ypad = 0.01 * max_intensity - threshold = label_threshold * max_intensity - by_series = defaultdict(list) - for peak in spectrum.peak_list: - height = peak[1] - if normalize: - height /= unscaled_max / 100.0 - if threshold >= height: - continue - height += ypad - if peak[2] and not isinstance(peak[2][0], (Unannotated, )): - annots = peak[2] - for annot in annots: - if isinstance(annot, InvalidAnnotation): - continue - if annot.series_label == 'peptide': - by_series[annot.series].append(peak) - else: - by_series[annot.series_label].append(peak) - txt = ax.text(peak[0], height, - ',\n'.join(filter(lambda x: x != '?', map(str, annots))), - ha='center', rotation=label_rotation, - clip_on=True) - txt.set_path_effects([path_effects.Stroke(linewidth=0.75, foreground='white'), - path_effects.Normal()]) - - for annot_series, peaks in by_series.items(): - sub_mz_array, sub_intensity_array = peaklist_to_vector(peaks) - - if normalize: - sub_intensity_array = sub_intensity_array / sub_intensity_array.max() * 100.0 - ax.plot( - sub_mz_array, - sub_intensity_array, - label=annot_series, - color=series_to_color[annot_series], - lw=2.0 - ) - - - ax.set_xlabel("m/z") - ax.set_ylabel("Relative Intensity") - ax.set_title(f"{spectrum.name}") - if pretty: - if intensity_array.shape[0] > 0: - set_ylim = intensity_array.min() >= 0 - else: - set_ylim = True - _beautify_axes(ax, set_ylim, normalize) - return ax - - -def _beautify_axes(ax, set_ylim=True, normalize=False): - ax.axes.spines['right'].set_visible(False) - ax.axes.spines['top'].set_visible(False) - ax.yaxis.tick_left() - ax.xaxis.tick_bottom() - ax.xaxis.set_ticks_position('none') - ax.get_xaxis().get_major_formatter().set_useOffset(False) - if set_ylim: - ax.set_ylim(0, max(ax.get_ylim())) - if normalize: - _normalize_ylabels(ax) - # ax.set_ylim(0, max(ax.get_ylim()) * 1.15) - xlim = ax.get_xlim() - ax.set_xlim(max(xlim[0] - 100, 0), xlim[1] + 50) - return ax - - -def _normalize_ylabels(ax, adjust_sign=True): - ytick_labels = ax.get_yticklabels() - yticks = ax.get_yticks() - for tl, tick in zip(ytick_labels, yticks): - txt = tl.get_text() - if txt == "": - txt = str(tick) - if adjust_sign: - txt = txt.replace("-", "") - txt += "%" - tl.set_text(txt) - ax.set_yticklabels(ytick_labels) - return ax diff --git a/implementations/python/mzlib/index/__init__.py b/implementations/python/mzlib/index/__init__.py deleted file mode 100644 index 197a26e..0000000 --- a/implementations/python/mzlib/index/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -from .memory import MemoryIndex -from .sql import SQLIndex -from .base import IndexBase \ No newline at end of file diff --git a/implementations/python/mzlib/index/base.py b/implementations/python/mzlib/index/base.py deleted file mode 100644 index b14c98e..0000000 --- a/implementations/python/mzlib/index/base.py +++ /dev/null @@ -1,134 +0,0 @@ -import warnings - -from typing import Collection, Iterator, Optional, Union, Any, List - - -class IndexRecordBase: - __slots__ = () - - number: int - index: int - offset: int - name: str - - -class IndexBase(Collection): - - @classmethod - def from_filename(cls, filename, library=None): - raise NotImplementedError() - - def offset_for(self, record_label) -> int: - record = self.record_for(record_label) - return record.offset - - def offset_for_cluster(self, record_label) -> int: - record = self.record_for_cluster(record_label) - return record.offset - - def record_for(self, record_label: Union[int, str]) -> IndexRecordBase: - record = self.search(record_label) - if isinstance(record, list): - warnings.warn( - f"Multiple records found for {record_label}, using the first") - record = record[0] - return record - - def record_for_cluster(self, record_label: int) -> IndexRecordBase: - record = self.search_clusters(record_label) - if isinstance(record, list): - warnings.warn( - f"Multiple records found for {record_label}, using the first") - record = record[0] - return record - - def search(self, i: Union[str, int, slice], **kwargs) -> Union[IndexRecordBase, List[IndexRecordBase]]: - raise NotImplementedError() - - def search_clusters(self, i: Optional[Union[int, slice]]=None, **kwargs) -> Union[IndexRecordBase, List[IndexRecordBase]]: - raise NotImplementedError() - - def add(self, number: int, offset: int, name: str, analyte: Any, attributes=None): - """ - Add a new entry to the spectrum index. - - Parameters - ---------- - number : int - A numerical identifier for this spectrum. - offset : int - The offset in the file to reach the spectrum (in bytes if appropriate) - name : str, - A text identifier for this spectrum. - analyte : str, optional - A text representation of the analyte for that record - attributes : Dict[str, Any], optional - A key-value pair collection of this record, currently not supported. - """ - raise NotImplementedError() - - def add_cluster(self, number: int, offset: int, attributes=None): - """ - Add a new entry to the spectrum index. - - Parameters - ---------- - number : int - A numerical identifier for this spectrum. - offset : int - The offset in the file to reach the spectrum (in bytes if appropriate) - attributes : Dict[str, Any], optional - A key-value pair collection of this record, currently not supported. - """ - raise NotImplementedError() - - def commit(self): - """ - Commit any index state to disk, if this index supports persistence. - - Has no effect on index types that do not have a persistence functionality. - """ - raise NotImplementedError() - - def iter_clusters(self) -> Iterator[IndexRecordBase]: - raise NotImplementedError() - - def iter_spectra(self) -> Iterator[IndexRecordBase]: - for i in range(len(self)): - yield self[i] - - def _get_by_index(self, i: Union[int, slice]) -> Union[IndexRecordBase, List[IndexRecordBase]]: - raise NotImplementedError() - - def __iter__(self): - return self.iter_spectra() - - def __getitem__(self, i: Union[int, str, slice]): - return self.search(i) - - def __len__(self): - raise NotImplementedError() - - def __contains__(self, key) -> bool: - try: - hit = self.search(key) - return True - except (KeyError, IndexError, ValueError): - return False - - def check_names_unique(self) -> bool: - """ - Checks that all indexed spectra have unique - ``spectrum name`` parameters. - - Returns - ------- - bool: - Whether the spectrum names in the index are unique. - """ - seen = set() - for record in self: - if record.name in seen: - return False - seen.add(record.name) - return True diff --git a/implementations/python/mzlib/index/memory.py b/implementations/python/mzlib/index/memory.py deleted file mode 100644 index a4b0d3f..0000000 --- a/implementations/python/mzlib/index/memory.py +++ /dev/null @@ -1,302 +0,0 @@ -import warnings -import logging - -from typing import Any, Dict, Iterator, Optional, List, DefaultDict, Union - -from numbers import Integral -from collections import defaultdict - -from mzlib.index.base import IndexRecordBase - -from .base import IndexBase, IndexRecordBase - -logger = logging.getLogger(__name__) -logger.addHandler(logging.NullHandler()) - - -class _IndexAttr: - __slots__ = () - - def get(self, key: str, default=None) -> Any: - if self.attributes is not None: - return self.attributes.get(key, default) - return default - - def set(self, key: str, value: Any): - if self.attributes is not None: - self.attributes[key] = value - else: - self.attributes = {key: value} - - -class IndexRecord(IndexRecordBase, _IndexAttr): - """ - A spectrum index record. - - Attributes - ---------- - number : int - A numerical identifier for the spectrum - offset : int - The offset in the file to reach the spectrum (in bytes if appropriate) - name : str, - A text identifier for this spectrum. - analyte : str, optional - A text representation of the analyte for that record - attributes : Dict[str, Any], optional - A key-value pair collection of this record. - """ - - __slots__ = ('number', 'offset', 'name', 'analyte', 'index', 'attributes') - - number: int - offset: int - name: str - index: int - analyte: Any - attributes: Optional[Dict[str, Any]] - - def __init__(self, number, offset, name, analyte, index: int=None, attributes=None): - self.number = number - self.offset = offset - self.name = name - self.analyte = analyte - self.index = index - self.attributes = attributes - - def __repr__(self): - template = f"{self.__class__.__name__}({self.number}, {self.offset}, {self.name}, {self.analyte}, {self.index}, {self.attributes})" - return template - - def __eq__(self, other): - if self.number != other.number: - return False - elif self.offset != other.offset: - return False - elif self.name != other.name: - return False - elif self.analyte != other.analyte: - return False - if bool(self.attributes) == bool(other.attributes): - if bool(self.attributes) and self.attributes != other.attributes: - return False - # Implicitly allow None and empty dictionaries to be the same - return True - - def __ne__(self, other): - return not self == other - - def __hash__(self): - return hash(self.name) - - def to_dict(self) -> Dict: - return { - k: getattr(self, k, None) for k in self.__slots__ - } - - @classmethod - def from_dict(cls, state: Dict) -> 'IndexRecord': - return cls(**state) - - -class ClusterIndexRecord(IndexRecordBase, _IndexAttr): - """ - A spectrum cluster index record. - - Attributes - ---------- - number : int - A numerical identifier for this spectrum. - offset : int - The offset in the file to reach the spectrum (in bytes if appropriate) - attributes : Dict[str, Any], optional - A key-value pair collection of this record - """ - - __slots__ = ('number', 'offset', 'attributes') - - def __init__(self, number, offset, attributes=None): - self.number = number - self.offset = offset - self.attributes = attributes - - def __repr__(self): - template = f"{self.__class__.__name__}({self.number}, {self.offset}, {self.attributes})" - return template - - def __eq__(self, other): - if self.number != other.number: - return False - elif self.offset != other.offset: - return False - if bool(self.attributes) == bool(other.attributes): - if bool(self.attributes) and self.attributes != other.attributes: - return False - # Implicitly allow None and empty dictionaries to be the same - return True - - def __ne__(self, other): - return not self == other - - def __hash__(self): - return hash(self.name) - - def to_dict(self) -> Dict: - return { - k: getattr(self, k, None) for k in self.__slots__ - } - - @classmethod - def from_dict(cls, state: Dict) -> 'ClusterIndexRecord': - return cls(**state) - - -class MemoryIndex(IndexBase): - records: List[IndexRecord] - cluster_records: List[ClusterIndexRecord] - metadata: Dict[str, Any] - - _dirty: bool - _by_key: Dict[int, IndexRecord] - _by_key_cluster: Dict[int, ClusterIndexRecord] - _by_name: DefaultDict[str, List[IndexRecord]] - _by_attr: DefaultDict[str, DefaultDict[Any, List[IndexRecord]]] - - @classmethod - def from_filename(cls, filename, library=None): - inst = cls() - return inst, False - - def __init__(self, records=None, cluster_records=None, metadata=None): - self.records = list(records or []) - self.cluster_records = list(cluster_records or []) - self._by_name = defaultdict(list) - self._by_key = {} - self._by_key_cluster = {} - self._by_attr = defaultdict(lambda: defaultdict(list)) - self.metadata = metadata or {} - self._dirty = True - - def iter_clusters(self) -> Iterator[IndexRecordBase]: - """Iterate over cluster entries in the index.""" - return iter(self.cluster_records) - - def iter_spectra(self): - """Iterate over spectrum entries in the index.""" - return iter(self.records) - - def __len__(self): - return len(self.records) - - def search(self, i=None, **kwargs): - if self._dirty: - self._update_index() - if i is None and kwargs: - # Executing attribute query - raise NotImplementedError() - if isinstance(i, Integral): - try: - return self._by_key[i] - except IndexError as err: - raise KeyError(i) from err - elif isinstance(i, slice): - start = i.start - stop = i.stop - if start is None: - start = min(self._by_key) if self._by_key else 0 - if stop is None: - stop = max(self._by_key) if self._by_key else 0 - return [self._by_key[i] for i in range(start, stop) if i in self._by_key] - if i in self._by_name: - records = self._by_name[i] - if len(records) == 1: - return records[0] - else: - return records - else: - raise KeyError(i) - - def search_clusters(self, i=None, **kwargs): - if self._dirty: - self._update_index() - - if i is None and kwargs: - # Executing attribute query - raise NotImplementedError() - - if isinstance(i, Integral): - return self._by_key_cluster[i] - - elif isinstance(i, slice): - start = i.start - stop = i.stop - if start is None: - start = min(self._by_key_cluster) if self._by_key_cluster else 0 - if stop is None: - stop = max(self._by_key_cluster) if self._by_key_cluster else 0 - return [self._by_key_cluster[i] for i in range(start, stop) if i in self._by_key_cluster] - - def __getitem__(self, i): - return self._get_by_index(i) - - def _get_by_index(self, i: Union[int, slice]) -> Union[IndexRecord, List[IndexRecord]]: - return self.records[i] - - def _update_index(self): - self.records.sort(key=lambda x: x.number) - - self._by_key.clear() - self._by_name = defaultdict(list) - for record in self: - self._by_key[record.number] = record - self._by_name[record.name].append(record) - - self.cluster_records.sort(key=lambda x: x.number) - self._by_key_cluster.clear() - for record in self.cluster_records: - self._by_key_cluster[record.number] = record - - self._dirty = False - - def add(self, number: int, offset: int, name: str, analyte: Any, attributes=None): - """ - Add a new entry to the spectrum index. - - Parameters - ---------- - number : int - A numerical identifier for this spectrum. - offset : int - The offset in the file to reach the spectrum (in bytes if appropriate) - name : str, - A text identifier for this spectrum. - analyte : str, optional - A text representation of the analyte for that record - attributes : Dict[str, Any], optional - A key-value pair collection of this record, currently not supported. - """ - n = len(self.records) - record = IndexRecord(number, offset, name, analyte, n, attributes) - self.records.append(record) - self._dirty = True - - def add_cluster(self, number: int, offset: int, attributes=None): - """ - Add a new entry to the spectrum index. - - Parameters - ---------- - number : int - A numerical identifier for this spectrum. - offset : int - The offset in the file to reach the spectrum (in bytes if appropriate) - attributes : Dict[str, Any], optional - A key-value pair collection of this record, currently not supported. - """ - record = ClusterIndexRecord(number, offset, attributes) - self.cluster_records.append(record) - self._dirty = True - - - def commit(self): - self._update_index() diff --git a/implementations/python/mzlib/index/sql.py b/implementations/python/mzlib/index/sql.py deleted file mode 100644 index 24cc10b..0000000 --- a/implementations/python/mzlib/index/sql.py +++ /dev/null @@ -1,257 +0,0 @@ -import io -import os -import numbers -import pathlib -import logging -from typing import Iterator, List, Union - -from sqlalchemy import Column, ForeignKey, Integer, Float, String, DateTime, Text, LargeBinary - -from mzlib.index.base import IndexRecordBase -try: # For SQLAlchemy 2.0 - from sqlalchemy.orm import declarative_base -except ImportError: - from sqlalchemy.ext.declarative import declarative_base -from sqlalchemy.orm import relationship -from sqlalchemy.engine import Engine -from sqlalchemy import create_engine, func -from sqlalchemy.orm import sessionmaker, scoped_session - -from .base import IndexBase - - -logger = logging.getLogger(__name__) -logger.addHandler(logging.NullHandler()) - - -Base = declarative_base() - -#### Define the database tables as classes - - -class SpectrumLibraryIndexAttribute(Base): - __tablename__ = 'spectrum_library_index_attribute' - id = Column(Integer, primary_key=True) - name = Column(String(255), nullable=False) - value = Column(String(1024), nullable=False) - - -#### Define the database tables as classes -class SpectrumLibraryIndexRecord(Base): - __tablename__ = 'spectrum_library_index_record' - id = Column(Integer, primary_key=True) - number = Column(Integer, nullable=False, index=True) - offset = Column(Integer, nullable=False) - name = Column(String(1024), nullable=False) - index = Column(Integer, nullable=False, index=True) - analyte = Column(String(2014), nullable=True) - - def __repr__(self): - return f"{self.__class__.__name__}({self.number}, {self.offset}, {self.name}, {self.analyte})" - - -class ClusterSpectrumLibraryIndexRecord(Base): - __tablename__ = 'cluster_spectrum_library_index_record' - id = Column(Integer, primary_key=True) - number = Column(Integer, nullable=False, index=True) - offset = Column(Integer, nullable=False) - - def __repr__(self): - return f"{self.__class__.__name__}({self.number}, {self.offset}, {self.name}, {self.analyte})" - - -class SQLIndex(IndexBase): - extension = '.splindex' - - filename: str - index_filename: str - _cache: SpectrumLibraryIndexRecord - session: scoped_session - engine: Engine - - @classmethod - def from_filename(cls, filename, library=None): - if not isinstance(filename, (str, pathlib.Path)): - if not hasattr(filename, "name"): - raise TypeError(f"Could not coerce filename from {filename}") - else: - filename = filename.name - exists = os.path.exists(filename + cls.extension) - inst = cls(filename) - - # File was empty - if len(inst) == 0 and exists: - exists = False - return inst, exists - - @classmethod - def exists(cls, filename: Union[str, pathlib.Path, io.FileIO]): - if not isinstance(filename, (str, pathlib.Path)): - if not hasattr(filename, "name"): - raise TypeError(f"Could not coerce filename from {filename}") - else: - filename = filename.name - exists = os.path.exists(filename + cls.extension) - return exists - - def __init__(self, filename): - self.filename = filename - self.index_filename = self.filename + self.extension - self._cache = None - self.connect() - self._size = len(self) - self._size_uncommitted = 0 - - def connect(self, create=None): - filename = self.index_filename - if os.path.exists(filename): - if create: - logger.debug(f'INFO: Deleting previous index file {filename}') - os.remove(filename) - logger.debug(f'INFO: Creating index file {filename}') - engine = create_engine("sqlite:///"+filename) - Base.metadata.create_all(engine) - - session = scoped_session(sessionmaker(bind=engine)) - self.session = session - self.engine = engine - self._cache = None - - def add(self, number, offset, name, analyte=None, attributes=None): - """ - Add a new entry to the spectrum index. - - Parameters - ---------- - number : int - A numerical identifier for this spectrum. - offset : int - The offset in the file to reach the spectrum (in bytes if appropriate) - name : str, - A text identifier for this spectrum. - analyte : str, optional - A text representation of the analyte for that record - attributes : Dict[str, Any], optional - A key-value pair collection of this record, currently not supported. - """ - record = SpectrumLibraryIndexRecord(number=number, offset=offset, name=name, - index=self._size + self._size_uncommitted, analyte=analyte) - self._size_uncommitted += 1 - if attributes is not None: - raise NotImplementedError("Record attribute storage is not implemented") - self.session.add(record) - - def add_cluster(self, number: int, offset: int, attributes=None): - """ - Add a new entry to the spectrum index. - - Parameters - ---------- - number : int - A numerical identifier for this spectrum. - offset : int - The offset in the file to reach the spectrum (in bytes if appropriate) - attributes : Dict[str, Any], optional - A key-value pair collection of this record, currently not supported. - """ - record = ClusterSpectrumLibraryIndexRecord(number=number, offset=offset) - if attributes is not None: - raise NotImplementedError("Record attribute storage is not implemented") - self.session.add(record) - - def commit(self): - """Persist any new entries to disk.""" - self._size += self._size_uncommitted - self._size_uncommitted = 0 - self.session.commit() - - def iter_clusters(self) -> Iterator[IndexRecordBase]: - """Iterate over cluster entries in the index.""" - for record in self.session.query(ClusterSpectrumLibraryIndexRecord).order_by( - ClusterSpectrumLibraryIndexRecord.number).yield_per(10000): - yield record - - def iter_spectra(self): - """Iterate over spectrum entries in the index.""" - for record in self.session.query(SpectrumLibraryIndexRecord).order_by( - SpectrumLibraryIndexRecord.number).yield_per(10000): - yield record - - def __getitem__(self, i): - return self._get_by_index(i) - - def _get_by_index(self, i: Union[int, slice]) -> Union[SpectrumLibraryIndexRecord, List[SpectrumLibraryIndexRecord]]: - if isinstance(i, slice): - records = self.session.query(SpectrumLibraryIndexRecord).slice(i.start, i.stop).all() - if i.step: - raise NotImplementedError() - return records - else: - record = self.session.query(SpectrumLibraryIndexRecord).offset(i).limit(1).first() - return record - - def __len__(self): - value = self.session.query(func.count(SpectrumLibraryIndexRecord.id)).scalar() - return value - - def search(self, i, **kwargs): - if i is None and kwargs: - # Executing attribute query - raise NotImplementedError() - if isinstance(i, numbers.Integral): - if i < 0: - i = len(self) + i - if self._cache is not None and self._cache.number == i: - return self._cache - records = self.session.query(SpectrumLibraryIndexRecord).filter(SpectrumLibraryIndexRecord.number == i).all() - - if len(records) == 1: - return records[0] - elif len(records) == 0: - raise IndexError(i) - else: - raise ValueError(f"Too many records found for spectrum number {i}") - elif isinstance(i, slice): - start = i.start or 0 - end = i.stop or float('inf') - records = self.session.query(SpectrumLibraryIndexRecord).filter( - SpectrumLibraryIndexRecord.number >= start, - SpectrumLibraryIndexRecord.number < end).all() - return records - else: - records = self.session.query(SpectrumLibraryIndexRecord).filter( - SpectrumLibraryIndexRecord.name == i).all() - if not records: - raise KeyError(i) - elif len(records) == 1: - return records[0] - else: - return records - - def search_clusters(self, i, **kwargs): - if i is None and kwargs: - # Executing attribute query - raise NotImplementedError() - if isinstance(i, numbers.Integral): - if i < 0: - i = len(self) + i - if self._cache is not None and self._cache.number == i: - return self._cache - records = self.session.query(ClusterSpectrumLibraryIndexRecord).filter( - ClusterSpectrumLibraryIndexRecord.number == i).all() - - if len(records) == 1: - return records[0] - elif len(records) == 0: - raise IndexError(i) - else: - raise ValueError(f"Too many records found for spectrum number {i}") - elif isinstance(i, slice): - start = i.start or 0 - end = i.stop or float('inf') - records = self.session.query(ClusterSpectrumLibraryIndexRecord).filter( - ClusterSpectrumLibraryIndexRecord.number >= start, - ClusterSpectrumLibraryIndexRecord.number < end).all() - return records - else: - raise NotImplementedError() diff --git a/implementations/python/mzlib/obo/psi-ms.obo b/implementations/python/mzlib/obo/psi-ms.obo deleted file mode 100644 index 741bce1..0000000 --- a/implementations/python/mzlib/obo/psi-ms.obo +++ /dev/null @@ -1,22132 +0,0 @@ -format-version: 1.2 -data-version: 4.1.57 -date: 21:05:2021 00:00 -saved-by: Joshua Klein -auto-generated-by: OBO-Edit 2.3.1 -import: http://ontologies.berkeleybop.org/pato.obo -import: http://ontologies.berkeleybop.org/uo.obo -default-namespace: MS -namespace-id-rule: * MS:$sequence(7,0,9999999)$ -namespace-id-rule: * PEFF:$sequence(7,0,9999999)$ -remark: namespace: MS -remark: namespace: PEFF -remark: coverage: Mass spectrometer output files and spectra interpretation -remark: creator: Yasset Perez-Riverol ebi.ac.uk> -remark: creator: Matt Chambers vanderbilt.edu> -remark: creator: Andreas Bertsch informatik.uni-tuebingen.de> -remark: creator: Marius Kallhardt bdal.de> -remark: creator: Eric Deutsch systemsbiology.org> -remark: creator: Fredrik Levander immun.lth.se> -remark: creator: Pierre-Alain Binz chuv.ch> -remark: creator: Gerhard Mayer rub.de> -remark: creator: Joshua Klein bu.edu> -remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group -remark: When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page -remark: For any queries contact psidev-ms-vocab@lists.sourceforge.net -remark: URL: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo -remark: This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. -remark: To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. -ontology: ms - -[Typedef] -id: has_regexp -name: has regexp - -[Typedef] -id: has_units -name: has_units - -[Typedef] -id: part_of -name: part_of -is_transitive: true - -[Typedef] -id: has_order -name: has_order - -[Typedef] -id: has_domain -name: has_domain - -[Typedef] -id: has_value_type -name: has value type -def: "'Entity A' has value type 'Entity B', such as xsd:float." [] - -[Term] -id: MS:0000000 -name: Proteomics Standards Initiative Mass Spectrometry Vocabularies -def: "Proteomics Standards Initiative Mass Spectrometry Vocabularies." [PSI:MS] - -[Term] -id: MS:1000001 -name: sample number -def: "A reference number relevant to the sample under study." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000548 ! sample attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000002 -name: sample name -def: "A reference string relevant to the sample under study." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000548 ! sample attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000003 -name: sample state -def: "The chemical phase of a pure sample, or the state of a mixed sample." [PSI:MS] -is_a: MS:1000548 ! sample attribute - -[Term] -id: MS:1000004 -name: sample mass -def: "Total mass of sample used." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000548 ! sample attribute -relationship: has_units UO:0000021 ! gram -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000005 -name: sample volume -def: "Total volume of solution used." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000548 ! sample attribute -relationship: has_units UO:0000098 ! milliliter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000006 -name: sample concentration -def: "Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000548 ! sample attribute -relationship: has_units UO:0000175 ! gram per liter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000007 -name: inlet type -def: "The nature of the sample inlet." [PSI:MS] -relationship: part_of MS:1000458 ! source - -[Term] -id: MS:1000008 -name: ionization type -def: "The method by which gas phase ions are generated from the sample." [PSI:MS] -relationship: part_of MS:1000458 ! source - -[Term] -id: MS:1000009 -name: ionization mode -def: "OBSOLETE Whether positive or negative ions are selected for analysis by the spectrometer." [PSI:MS] -comment: This term was made obsolete because it was replaced by scan polarity (MS:1000465). -is_obsolete: true - -[Term] -id: MS:1000010 -name: analyzer type -def: "OBSOLETE The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000011 -name: mass resolution -def: "Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000503 ! scan attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000012 -name: resolution measurement method -def: "Which of the available standard measures is used to define whether two peaks are separate." [PSI:MS] -is_a: MS:1000596 ! measurement method - -[Term] -id: MS:1000013 -name: resolution type -def: "OBSOLETE Specify the nature of resolution for the mass analyzer. Resolution is usually either constant with respect to m/z or proportional to m/z." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000014 -name: accuracy -def: "Accuracy is the degree of conformity of a measured mass to its actual value." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000480 ! mass analyzer attribute -relationship: has_units MS:1000040 ! m/z -relationship: has_units UO:0000169 ! parts per million -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000015 -name: scan rate -def: "Rate in Th/sec for scanning analyzers." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000503 ! scan attribute -relationship: has_units MS:1000807 ! Th/s -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000016 -name: scan start time -def: "The time that an analyzer started a scan, relative to the start of the MS run." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000503 ! scan attribute -is_a: MS:1002345 ! PSM-level attribute -relationship: has_units UO:0000010 ! second -relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000017 -name: Scan Function -def: "OBSOLETE Describes the type of mass analysis being performed. Two primary modes are: typical acquisition over a range of masses (Mass Scan), and Selected Ion Detection. The primary difference is that Selected Ion Detection produces a single value for the signal at the selected mass rather than producing a mass spectrum." [PSI:MS] -comment: OBSOLETE This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000018 -name: scan direction -def: "Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low)." [PSI:MS] -relationship: part_of MS:1000441 ! scan - -[Term] -id: MS:1000019 -name: scan law -def: "Describes the function in control of the m/z scan (for scanning instruments). Commonly the scan function is linear, but in principle any function can be used." [PSI:MS] -relationship: part_of MS:1000441 ! scan - -[Term] -id: MS:1000020 -name: scanning method -def: "Describes the acquisition data type produced by a tandem mass spectrometry experiment." [PSI:MS] -comment: OBSOLETE This former purgatory term was made obsolete. -synonym: "Tandem Scanning Method" RELATED [] -is_obsolete: true - -[Term] -id: MS:1000021 -name: reflectron state -def: "Status of the reflectron, turned on or off." [PSI:MS] -is_a: MS:1000480 ! mass analyzer attribute - -[Term] -id: MS:1000022 -name: TOF Total Path Length -def: "The length of the field free drift space in a time of flight mass spectrometer." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000480 ! mass analyzer attribute -relationship: has_units UO:0000008 ! meter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000023 -name: isolation width -def: "OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion." [PSI:MS] -comment: This former purgatory term was made obsolete. -xref: value-type:xsd\:float "The allowed value-type for this CV term." -relationship: has_units MS:1000040 ! m/z -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000024 -name: final MS exponent -def: "Final MS level achieved when performing PFF with the ion trap (e.g. MS E10)." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1000480 ! mass analyzer attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1000025 -name: magnetic field strength -def: "A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity." [PSI:MS] -synonym: "B" EXACT [] -synonym: "Magnetic Field" RELATED [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000480 ! mass analyzer attribute -relationship: has_units UO:0000228 ! tesla -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000026 -name: detector type -def: "Type of detector used in the mass spectrometer." [PSI:MS] -relationship: part_of MS:1000453 ! detector - -[Term] -id: MS:1000027 -name: detector acquisition mode -def: "Method by which detector signal is acquired by the data system." [PSI:MS] -relationship: part_of MS:1000453 ! detector - -[Term] -id: MS:1000028 -name: detector resolution -def: "The resolving power of the detector to detect the smallest difference between two ions so that the valley between them is a specified fraction of the peak height." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000481 ! detector attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000029 -name: sampling frequency -def: "The rate of signal sampling (measurement) with respect to time." [PSI:MS] -synonym: "ADC Sampling Frequency" NARROW [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000481 ! detector attribute -relationship: has_units UO:0000106 ! hertz -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000030 -name: vendor -def: "OBSOLETE Name of instrument vendor." [PSI:MS] -comment: This term was made obsolete because it was replaced by instrument model (MS:1000031). -is_obsolete: true - -[Term] -id: MS:1000031 -name: instrument model -def: "Instrument model name not including the vendor's name." [PSI:MS] -relationship: part_of MS:1000463 ! instrument - -[Term] -id: MS:1000032 -name: customization -def: "Free text description of a single customization made to the instrument; for several modifications, use several entries." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000496 ! instrument attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000033 -name: deisotoping -def: "The removal of isotope peaks to represent the fragment ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution." [PSI:MS] -is_a: MS:1000543 ! data processing action - -[Term] -id: MS:1000034 -name: charge deconvolution -def: "The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions." [PSI:MS] -is_a: MS:1000543 ! data processing action - -[Term] -id: MS:1000035 -name: peak picking -def: "Spectral peak processing conducted on the acquired data to convert profile data to centroided data." [PSI:MS] -is_a: MS:1000543 ! data processing action - -[Term] -id: MS:1000036 -name: scan mode -def: "OBSOLETE." [PSI:MS] -comment: This term was made obsolete because . -is_obsolete: true - -[Term] -id: MS:1000037 -name: polarity -def: "OBSOLETE Terms to describe the polarity setting of the instrument." [PSI:MS] -comment: This term was made obsolete because it was redundant with the Pato Ontology term polarity (UO:0002186). -is_obsolete: true - -[Term] -id: MS:1000038 -name: minute -def: "OBSOLETE Acquisition time in minutes." [PSI:MS] -comment: This term was made obsolete because it was redundant with Unit Ontology minute (UO:0000031). -is_obsolete: true - -[Term] -id: MS:1000039 -name: second -def: "OBSOLETE Acquisition time in seconds." [PSI:MS] -comment: This term was made obsolete because it was redundant with Unit Ontology second (UO:0000010). -is_obsolete: true - -[Term] -id: MS:1000040 -name: m/z -def: "Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated." [PSI:MS] -synonym: "mass-to-charge ratio" EXACT [] -synonym: "Th" EXACT [] -synonym: "thomson" EXACT [] -is_a: UO:0000000 ! unit - -[Term] -id: MS:1000041 -name: charge state -def: "Number of net charges, positive or negative, on an ion." [PSI:MS] -synonym: "z" EXACT [] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1000455 ! ion selection attribute -is_a: MS:1000507 ! ion property -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1000042 -name: peak intensity -def: "Intensity of ions as measured by the height or area of a peak in a mass spectrum." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000455 ! ion selection attribute -relationship: has_units MS:1000131 ! number of detector counts -relationship: has_units MS:1000132 ! percent of base peak -relationship: has_units MS:1000814 ! counts per second -relationship: has_units MS:1000905 ! percent of base peak times 100 -relationship: has_units UO:0000269 ! absorbance unit -relationship: part_of MS:1000231 ! peak -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000043 -name: intensity unit -def: "Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors." [PSI:MS] -is_a: UO:0000000 ! unit - -[Term] -id: MS:1000044 -name: dissociation method -def: "Fragmentation method used for dissociation or fragmentation." [PSI:MS] -synonym: "Activation Method" RELATED [] -relationship: part_of MS:1000456 ! precursor activation - -[Term] -id: MS:1000045 -name: collision energy -def: "Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000510 ! precursor activation attribute -relationship: has_units UO:0000266 ! electronvolt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000046 -name: energy unit -def: "OBSOLETE Energy units are represented in either eV or Joules." [PSI:MS] -comment: This term was made obsolete because it was redundant with the Unit Ontology term energy unit (UO:0000111). -is_a: UO:0000000 ! unit -is_obsolete: true - -[Term] -id: MS:1000047 -name: emulsion -def: "State if the sample is in emulsion form." [PSI:MS] -is_a: MS:1000003 ! sample state - -[Term] -id: MS:1000048 -name: gaseous sample state -def: "State if the sample is in gaseous form." [PSI:MS] -is_a: MS:1000003 ! sample state - -[Term] -id: MS:1000049 -name: liquid sample state -def: "State if the sample is in liquid form." [PSI:MS] -is_a: MS:1000003 ! sample state - -[Term] -id: MS:1000050 -name: solid sample state -def: "State if the sample is in solid form." [PSI:MS] -is_a: MS:1000003 ! sample state - -[Term] -id: MS:1000051 -name: solution -def: "State if the sample is in solution form." [PSI:MS] -is_a: MS:1000003 ! sample state - -[Term] -id: MS:1000052 -name: suspension -def: "State if the sample is in suspension form." [PSI:MS] -is_a: MS:1000003 ! sample state - -[Term] -id: MS:1000053 -name: sample batch -def: "Sample batch lot identifier." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000548 ! sample attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000054 -name: chromatography -def: "OBSOLETE Chromatographic conditions used to obtain the sample." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000055 -name: continuous flow fast atom bombardment -def: "Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix." [PSI:MS] -synonym: "CF-FAB" EXACT [] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000056 -name: direct inlet -def: "The sample is directly inserted into the ion source, usually on the end of a heatable probe." [PSI:MS] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000057 -name: electrospray inlet -def: "Inlet used for introducing the liquid sample into an electrospray ionization source." [PSI:MS] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000058 -name: flow injection analysis -def: "Sample is directly injected or infused into the ionization source." [PSI:MS] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000059 -name: inductively coupled plasma -def: "A gas discharge ion source in which the energy to the plasma is supplied by electromagnetic induction." [PSI:MS] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000060 -name: infusion -def: "The continuous flow of solution of a sample into the ionization source." [PSI:MS] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000061 -name: jet separator -def: "A device that separates carrier gas from gaseous analyte molecules on the basis of diffusivity." [PSI:MS] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000062 -name: membrane separator -def: "A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane." [PSI:MS] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000063 -name: moving belt -def: "Continuous moving surface in the form of a belt which passes through an ion source carrying analyte molecules." [PSI:MS] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000064 -name: moving wire -def: "Continuous moving surface in the form of a wire which passes through an ion source carrying analyte molecules." [PSI:MS] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000065 -name: open split -def: "A division of flowing stream of liquid into two streams." [PSI:MS] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000066 -name: particle beam -def: "Method for generating ions from a solution of an analyte." [PSI:MS] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000067 -name: reservoir -def: "A sample inlet method involving a reservoir." [PSI:MS] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000068 -name: septum -def: "A disc composed of a flexible material that seals the entrance to the reservoir. Can also be entrance to the vacuum chamber." [PSI:MS] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000069 -name: thermospray inlet -def: "A method for generating gas phase ions from a solution of an analyte by rapid heating of the sample." [PSI:MS] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000070 -name: atmospheric pressure chemical ionization -def: "Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization." [PSI:MS] -synonym: "APCI" EXACT [] -is_a: MS:1000240 ! atmospheric pressure ionization - -[Term] -id: MS:1000071 -name: chemical ionization -def: "The formation of a new ion by the reaction of a neutral species with an ion. The process may involve transfer of an electron, a proton or other charged species between the reactants. When a positive ion results from chemical ionization the term may be used without qualification. When a negative ion results the term negative ion chemical ionization should be used. Note that this term is not synonymous with chemi-ionization." [PSI:MS] -synonym: "CI" EXACT [] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000072 -name: Electronic Ionization -def: "OBSOLETE The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended." [PSI:MS] -comment: This term was made obsolete because it was replaced by electron ionization (MS:1000389). -synonym: "EI" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000073 -name: electrospray ionization -def: "A process in which ionized species in the gas phase are produced from an analyte-containing solution via highly charged fine droplets, by means of spraying the solution from a narrow-bore needle tip at atmospheric pressure in the presence of a high electric field. When a pressurized gas is used to aid in the formation of a stable spray, the term pneumatically assisted electrospray ionization is used. The term ion spray is not recommended." [PSI:MS] -synonym: "ESI" EXACT [] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000074 -name: fast atom bombardment ionization -def: "The ionization of any species by the interaction of a focused beam of neutral atoms having a translational energy of several thousand eV with a sample that is typically dissolved in a solvent matrix. See also secondary ionization." [PSI:MS] -synonym: "FAB" EXACT [] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000075 -name: matrix-assisted laser desorption ionization -def: "The formation of gas-phase ions from molecules that are present in a solid or solvent matrix that is irradiated with a pulsed laser. See also laser desorption/ionization." [PSI:MS] -synonym: "MALDI" EXACT [] -is_a: MS:1000247 ! desorption ionization - -[Term] -id: MS:1000076 -name: negative ion mode -def: "OBSOLETE." [PSI:MS] -comment: This term was made obsolete because it was replaced by negative scan (MS:1000129). -is_obsolete: true - -[Term] -id: MS:1000077 -name: positive ion mode -def: "OBSOLETE." [PSI:MS] -comment: This term was made obsolete because it was replaced by positive scan (MS:1000130). -is_obsolete: true - -[Term] -id: MS:1000078 -name: axial ejection linear ion trap -def: "A linear ion trap mass spectrometer where ions are ejected along the axis of the analyzer." [PSI:MS] -is_a: MS:1000291 ! linear ion trap - -[Term] -id: MS:1000079 -name: fourier transform ion cyclotron resonance mass spectrometer -def: "A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z." [PSI:MS] -synonym: "FT_ICR" EXACT [] -is_a: MS:1000443 ! mass analyzer type - -[Term] -id: MS:1000080 -name: magnetic sector -def: "A device that produces a magnetic field perpendicular to a charged particle beam that deflects the beam to an extent that is proportional to the particle momentum per unit charge. For a monoenergetic beam, the deflection is proportional to m/z." [PSI:MS] -is_a: MS:1000443 ! mass analyzer type - -[Term] -id: MS:1000081 -name: quadrupole -def: "A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis." [PSI:MS] -is_a: MS:1000443 ! mass analyzer type - -[Term] -id: MS:1000082 -name: quadrupole ion trap -def: "Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials." [PSI:MS] -synonym: "Paul Ion trap" EXACT [] -synonym: "QIT" EXACT [] -synonym: "Quistor" EXACT [] -is_a: MS:1000264 ! ion trap - -[Term] -id: MS:1000083 -name: radial ejection linear ion trap -def: "A linear ion trap mass spectrometer where ions are ejected along the radius of the analyzer." [PSI:MS] -is_a: MS:1000291 ! linear ion trap - -[Term] -id: MS:1000084 -name: time-of-flight -def: "Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy." [PSI:MS] -synonym: "TOF" EXACT [] -is_a: MS:1000443 ! mass analyzer type - -[Term] -id: MS:1000085 -name: baseline -def: "An attribute of resolution when recording the detector response in absence of the analyte." [PSI:MS] -is_a: MS:1000012 ! resolution measurement method - -[Term] -id: MS:1000086 -name: full width at half-maximum -def: "A measure of resolution represented as width of the peak at half peak height." [PSI:MS] -synonym: "FWHM" EXACT [] -is_a: MS:1000012 ! resolution measurement method - -[Term] -id: MS:1000087 -name: ten percent valley -def: "An attribute of resolution when the ratio between adjacent signals is 10% of the signal height." [PSI:MS] -is_a: MS:1000012 ! resolution measurement method - -[Term] -id: MS:1000088 -name: constant -def: "OBSOLETE When resolution is constant with respect to m/z." [PSI:MS] -comment: This child of the former purgatory term resolution type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000089 -name: proportional -def: "OBSOLETE When resolution is proportional with respect to m/z." [PSI:MS] -comment: This child of the former purgatory term resolution type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000090 -name: mass scan -def: "OBSOLETE A variation of instrument where a selected mass is scanned." [PSI:MS] -comment: This child of the former purgatory term Scan Function was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000091 -name: selected ion detection -def: "OBSOLETE Please see Single Ion Monitoring." [PSI:MS] -comment: This child of the former purgatory term Scan Function was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000092 -name: decreasing m/z scan -def: "High to low direction in terms of m/z of the scan for scanning analyzers." [PSI:MS] -is_a: MS:1000018 ! scan direction - -[Term] -id: MS:1000093 -name: increasing m/z scan -def: "Low to high direction in terms of m/z of the scan for scanning analyzers." [PSI:MS] -is_a: MS:1000018 ! scan direction - -[Term] -id: MS:1000094 -name: exponential -def: "The mass scan is done in exponential mode." [PSI:MS] -is_a: MS:1000019 ! scan law - -[Term] -id: MS:1000095 -name: linear -def: "OBSOLETE The mass scan is done in linear mode." [PSI:MS] -comment: This term was made obsolete because it was redundant with the Pato Ontology term linear (UO:0001199). -is_a: MS:1000019 ! scan law -is_obsolete: true - -[Term] -id: MS:1000096 -name: quadratic -def: "The mass scan is done in quadratic mode." [PSI:MS] -is_a: MS:1000019 ! scan law - -[Term] -id: MS:1000097 -name: constant neutral mass loss -def: "OBSOLETE A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000098 -name: multiple ion monitoring -def: "OBSOLETE Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000099 -name: multiple reaction monitoring -def: "OBSOLETE This term is not recommended. See Selected Reaction Monitoring." [PSI:MS] -comment: This term was made obsolete because it was merged with selected reaction monitoring (MS:1000206). -synonym: "MRM" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000100 -name: precursor ion scan -def: "OBSOLETE The specific scan function or process that will record a precursor ion spectrum." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000101 -name: product ion scan -def: "OBSOLETE The specific scan function or process that records product ion spectrum." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000102 -name: single ion monitoring -def: "OBSOLETE The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum." [PSI:MS] -comment: This term was made obsolete because it was replaced by single ion monitoring (MS:100205). -is_obsolete: true - -[Term] -id: MS:1000103 -name: single reaction monitoring -def: "OBSOLETE This term is not recommended. See Selected Reaction Monitoring." [PSI:MS] -comment: This term was made obsolete because it was replaced by selected reaction monitoring (MS:1000206). -is_obsolete: true - -[Term] -id: MS:1000104 -name: None ?? -def: "OBSOLETE None." [PSI:MS] -comment: This term was made obsolete because . -is_obsolete: true - -[Term] -id: MS:1000105 -name: reflectron off -def: "Reflectron is off." [PSI:MS] -is_a: MS:1000021 ! reflectron state - -[Term] -id: MS:1000106 -name: reflectron on -def: "Reflectron is on." [PSI:MS] -is_a: MS:1000021 ! reflectron state - -[Term] -id: MS:1000107 -name: channeltron -def: "A horn-shaped (or cone-shaped) continuous dynode particle multiplier. The ion strikes the inner surface of the device and induces the production of secondary electrons that in turn impinge on the inner surfaces to produce more secondary electrons. This avalanche effect produces an increase in signal in the final measured current pulse." [PSI:MS] -synonym: "Channeltron Detector" EXACT [] -is_a: MS:1000026 ! detector type - -[Term] -id: MS:1000108 -name: conversion dynode electron multiplier -def: "A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected." [PSI:MS] -is_a: MS:1000346 ! conversion dynode - -[Term] -id: MS:1000109 -name: conversion dynode photomultiplier -def: "A detector in which ions strike a conversion dynode to produce electrons that in turn generate photons through a phosphorescent screen that are detected by a photomultiplier." [PSI:MS] -synonym: "ion-to-photon detector" RELATED [] -is_a: MS:1000346 ! conversion dynode - -[Term] -id: MS:1000110 -name: daly detector -def: "Detector consisting of a conversion dynode, scintillator and photomultiplier. The metal knob at high potential emits secondary electrons when ions impinge on the surface. The secondary electrons are accelerated onto the scintillator that produces light that is then detected by the photomultiplier detector." [PSI:MS] -synonym: "Daly" EXACT [] -is_a: MS:1000026 ! detector type - -[Term] -id: MS:1000111 -name: electron multiplier tube -def: "A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons." [PSI:MS] -synonym: "EMT" EXACT [] -is_a: MS:1000253 ! electron multiplier - -[Term] -id: MS:1000112 -name: faraday cup -def: "A conducting cup or chamber that intercepts a charged particle beam and is electrically connected to a current measuring device." [PSI:MS] -is_a: MS:1000026 ! detector type - -[Term] -id: MS:1000113 -name: focal plane array -def: "An array of detectors for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane." [PSI:MS] -is_a: MS:1000348 ! focal plane collector - -[Term] -id: MS:1000114 -name: microchannel plate detector -def: "A thin plate that contains a closely spaced array of channels that each act as a continuous dynode particle multiplier. A charged particle, fast neutral particle, or photon striking the plate causes a cascade of secondary electrons that ultimately exits the opposite side of the plate." [PSI:MS] -synonym: "multichannel plate" EXACT [] -is_a: MS:1000345 ! array detector - -[Term] -id: MS:1000115 -name: multi-collector -def: "A detector system commonly used in inductively coupled plasma mass spectrometers." [PSI:MS] -is_a: MS:1000026 ! detector type - -[Term] -id: MS:1000116 -name: photomultiplier -def: "A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected." [PSI:MS] -synonym: "PMT" EXACT [] -is_a: MS:1000026 ! detector type - -[Term] -id: MS:1000117 -name: analog-digital converter -def: "Analog-to-digital converter (abbreviated ADC, A/D or A to D) is an electronic integrated circuit (i/c) that converts continuous signals to discrete digital numbers." [PSI:MS] -synonym: "ADC" EXACT [] -is_a: MS:1000027 ! detector acquisition mode - -[Term] -id: MS:1000118 -name: pulse counting -def: "Definition to do." [PSI:MS] -is_a: MS:1000027 ! detector acquisition mode - -[Term] -id: MS:1000119 -name: time-digital converter -def: "A device for converting a signal of sporadic pluses into a digital representation of their time indices." [PSI:MS] -synonym: "TDC" EXACT [] -is_a: MS:1000027 ! detector acquisition mode - -[Term] -id: MS:1000120 -name: transient recorder -def: "A detector acquisition mode used for detecting transient signals." [PSI:MS] -is_a: MS:1000027 ! detector acquisition mode - -[Term] -id: MS:1000121 -name: SCIEX instrument model -def: "The brand of instruments from the joint venture between Applied Biosystems and MDS Analytical Technologies (formerly MDS SCIEX). Previously branded as \"Applied Biosystems|MDS SCIEX\"." [PSI:MS] -synonym: "Applied Biosystems|MDS SCIEX" RELATED [] -is_a: MS:1000031 ! instrument model - -[Term] -id: MS:1000122 -name: Bruker Daltonics instrument model -def: "Bruker Daltonics' instrument model." [PSI:MS] -is_a: MS:1000031 ! instrument model - -[Term] -id: MS:1000123 -name: IonSpec instrument model -def: "IonSpec corporation instrument model." [PSI:MS] -is_a: MS:1000489 ! Varian instrument model - -[Term] -id: MS:1000124 -name: Shimadzu instrument model -def: "Shimadzu corporation instrument model." [PSI:MS] -is_a: MS:1000031 ! instrument model - -[Term] -id: MS:1000125 -name: Thermo Finnigan instrument model -def: "ThermoFinnigan from Thermo Electron Corporation instrument model." [PSI:MS] -is_a: MS:1000483 ! Thermo Fisher Scientific instrument model - -[Term] -id: MS:1000126 -name: Waters instrument model -def: "Waters Corporation instrument model." [PSI:MS] -is_a: MS:1000031 ! instrument model - -[Term] -id: MS:1000127 -name: centroid spectrum -def: "Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset." [PSI:MS] -synonym: "Discrete Mass Spectrum" EXACT [] -is_a: MS:1000525 ! spectrum representation - -[Term] -id: MS:1000128 -name: profile spectrum -def: "A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis." [PSI:MS] -synonym: "continuous mass spectrum" EXACT [] -synonym: "Continuum Mass Spectrum" EXACT [] -is_a: MS:1000525 ! spectrum representation - -[Term] -id: MS:1000129 -name: negative scan -def: "Polarity of the scan is negative." [PSI:MS] -is_a: MS:1000465 ! scan polarity -is_a: MS:1000808 ! chromatogram attribute - -[Term] -id: MS:1000130 -name: positive scan -def: "Polarity of the scan is positive." [PSI:MS] -is_a: MS:1000465 ! scan polarity -is_a: MS:1000808 ! chromatogram attribute - -[Term] -id: MS:1000131 -name: number of detector counts -def: "The number of counted events observed in one or a group of elements of a detector." [PSI:MS] -is_a: MS:1000043 ! intensity unit - -[Term] -id: MS:1000132 -name: percent of base peak -def: "The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000043 ! intensity unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000133 -name: collision-induced dissociation -def: "The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended." [PSI:MS] -synonym: "CID" EXACT [] -synonym: "CAD" EXACT [] -synonym: "collisionally activated dissociation" EXACT [] -is_a: MS:1000044 ! dissociation method - -[Term] -id: MS:1000134 -name: plasma desorption -def: "The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization." [PSI:MS] -synonym: "PD" EXACT [] -is_a: MS:1000044 ! dissociation method - -[Term] -id: MS:1000135 -name: post-source decay -def: "A technique specific to reflectron time-of-flight mass spectrometers where product ions of metastable transitions or collision-induced dissociations generated in the drift tube prior to entering the reflectron are m/z separated to yield product ion spectra." [PSI:MS] -synonym: "PSD" EXACT [] -is_a: MS:1000044 ! dissociation method - -[Term] -id: MS:1000136 -name: surface-induced dissociation -def: "Fragmentation that results from the collision of an ion with a surface." [PSI:MS] -synonym: "SID" EXACT [] -is_a: MS:1000044 ! dissociation method - -[Term] -id: MS:1000137 -name: electron volt -def: "OBSOLETE A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J." [PSI:MS] -comment: This term was made obsolete because it was redundant with the Unit Ontology term electron volt (UO:0000266). -is_obsolete: true - -[Term] -id: MS:1000138 -name: normalized collision energy -def: "Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000510 ! precursor activation attribute -relationship: has_units UO:0000187 ! percent -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000139 -name: 4000 QTRAP -def: "Applied Biosystems/MDS SCIEX Q 4000 TRAP MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000140 -name: 4700 Proteomics Analyzer -def: "Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS." [PSI:MS] -is_a: MS:1000495 ! Applied Biosystems instrument model - -[Term] -id: MS:1000141 -name: apex IV -def: "Bruker Daltonics' apex IV: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS] -is_a: MS:1001556 ! Bruker Daltonics apex series - -[Term] -id: MS:1000142 -name: apex Q -def: "Bruker Daltonics' apex Q: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS] -is_a: MS:1001556 ! Bruker Daltonics apex series - -[Term] -id: MS:1000143 -name: API 150EX -def: "Applied Biosystems/MDS SCIEX API 150EX MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000144 -name: API 150EX Prep -def: "Applied Biosystems/MDS SCIEX API 150EX Prep MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000145 -name: API 2000 -def: "Applied Biosystems/MDS SCIEX API 2000 MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000146 -name: API 3000 -def: "Applied Biosystems/MDS SCIEX API 3000 MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000147 -name: API 4000 -def: "Applied Biosystems/MDS SCIEX API 4000 MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000148 -name: autoflex II -def: "Bruker Daltonics' autoflex II: MALDI TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1000149 -name: autoflex TOF/TOF -def: "Bruker Daltonics' autoflex TOF/TOF MS: MALDI TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1000150 -name: Auto Spec Ultima NT -def: "Waters magnetic sector based AutoSpec Ultima NT MS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1000151 -name: BioTOF II -def: "Bruker Daltonics' BioTOF II: ESI TOF." [PSI:MS] -is_a: MS:1001535 ! Bruker Daltonics BioTOF series - -[Term] -id: MS:1000152 -name: BioTOF-Q -def: "Bruker Daltonics' BioTOF-Q: ESI Q-TOF." [PSI:MS] -is_a: MS:1001535 ! Bruker Daltonics BioTOF series - -[Term] -id: MS:1000153 -name: DELTA plusAdvantage -def: "ThermoFinnigan DELTA plusAdvantage MS." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000154 -name: DELTAplusXP -def: "ThermoFinnigan DELTAplusXP MS." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000155 -name: ELEMENT2 -def: "OBSOLETE ThermoFinnigan ELEMENT2 MS." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000156 -name: esquire 4000 -def: "Bruker Daltonics' esquire 4000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI." [PSI:MS] -is_a: MS:1001533 ! Bruker Daltonics esquire series - -[Term] -id: MS:1000157 -name: esquire 6000 -def: "Bruker Daltonics' esquire 6000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI." [PSI:MS] -is_a: MS:1001533 ! Bruker Daltonics esquire series - -[Term] -id: MS:1000158 -name: explorer -def: "IonSpec Explorer MS." [PSI:MS] -is_a: MS:1000123 ! IonSpec instrument model - -[Term] -id: MS:1000159 -name: GCT -def: "Waters oa-ToF based GCT." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1000160 -name: HCT -def: "Bruker Daltonics' HCT: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] -is_a: MS:1000697 ! Bruker Daltonics HCT Series - -[Term] -id: MS:1000161 -name: HCTplus -def: "Bruker Daltonics' HCTplus: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] -is_a: MS:1000697 ! Bruker Daltonics HCT Series - -[Term] -id: MS:1000162 -name: HiRes ESI -def: "IonSpec HiResESI MS." [PSI:MS] -is_a: MS:1000123 ! IonSpec instrument model - -[Term] -id: MS:1000163 -name: HiRes MALDI -def: "IonSpec HiResMALDI MS." [PSI:MS] -is_a: MS:1000123 ! IonSpec instrument model - -[Term] -id: MS:1000164 -name: IsoPrime -def: "Waters IsoPrime MS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1000165 -name: IsoProbe -def: "Waters IsoProbe MS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1000166 -name: IsoProbe T -def: "Waters IsoProbe T MS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1000167 -name: LCQ Advantage -def: "ThermoFinnigan LCQ Advantage MS." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000168 -name: LCQ Classic -def: "ThermoFinnigan LCQ Classic MS." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000169 -name: LCQ Deca XP Plus -def: "ThermoFinnigan LCQ Deca XP Plus MS." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000170 -name: M@LDI L -def: "Waters oa-ToF based MALDI L." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1000171 -name: M@LDI LR -def: "Waters oa-ToF based MALDI LR." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1000172 -name: MAT253 -def: "ThermoFinnigan MAT253 MS." [PSI:MS] -is_a: MS:1000493 ! Finnigan MAT instrument model - -[Term] -id: MS:1000173 -name: MAT900XP -def: "ThermoFinnigan MAT900XP MS." [PSI:MS] -is_a: MS:1000493 ! Finnigan MAT instrument model - -[Term] -id: MS:1000174 -name: MAT900XP Trap -def: "ThermoFinnigan MAT900XP Trap MS." [PSI:MS] -is_a: MS:1000493 ! Finnigan MAT instrument model - -[Term] -id: MS:1000175 -name: MAT95XP -def: "ThermoFinnigan MAT95XP MS." [PSI:MS] -is_a: MS:1000493 ! Finnigan MAT instrument model - -[Term] -id: MS:1000176 -name: MAT95XP Trap -def: "ThermoFinnigan MAT95XP Trap MS." [PSI:MS] -is_a: MS:1000493 ! Finnigan MAT instrument model - -[Term] -id: MS:1000177 -name: microflex -def: "Bruker Daltonics' microflex: MALDI TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1000178 -name: microTOF LC -def: "Bruker Daltonics' microTOF LC: ESI TOF, Nanospray, APCI, APPI." [PSI:MS] -is_a: MS:1001536 ! Bruker Daltonics micrOTOF series - -[Term] -id: MS:1000179 -name: neptune -def: "ThermoFinnigan NEPTUNE MS." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000180 -name: NG-5400 -def: "Waters NG-5400 MS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1000181 -name: OMEGA -def: "IonSpec OMEGA MS." [PSI:MS] -is_a: MS:1000123 ! IonSpec instrument model - -[Term] -id: MS:1000182 -name: OMEGA-2001 -def: "IonSpec OMEGA-2001 MS." [PSI:MS] -is_a: MS:1000123 ! IonSpec instrument model - -[Term] -id: MS:1000183 -name: OmniFlex -def: "Bruker Daltonics' OmniFlex: MALDI TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1000184 -name: Platform ICP -def: "Waters Platform ICP MS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1000185 -name: PolarisQ -def: "ThermoFinnigan PolarisQ MS." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000186 -name: proteomics solution 1 -def: "Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000187 -name: Q TRAP -def: "Applied Biosystems/MDS SCIEX Q TRAP MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000188 -name: Q-Tof micro -def: "Waters oa-ToF based Q-Tof micro." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1000189 -name: Q-Tof Ultima -def: "Waters oa-ToF based Q-Tof Ultima." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1000190 -name: QSTAR -def: "Applied Biosystems/MDS SCIEX QSTAR MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000191 -name: quattro micro -def: "Waters (triple) quadrupole based micro." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1000192 -name: Quattro Ultima -def: "Waters (triple) quadrupole based Ultima." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1000193 -name: Surveyor MSQ -def: "ThermoFinnigan Surveyor MSQ MS." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000194 -name: SymBiot I -def: "Applied Biosystems/MDS SCIEX SymBiot I MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000195 -name: SymBiot XVI -def: "Applied Biosystems/MDS SCIEX SymBiot XVI MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000196 -name: TEMPUS TOF -def: "ThermoFinnigan TEMPUS TOF MS." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000197 -name: TRACE DSQ -def: "ThermoFinnigan TRACE DSQ MS." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000198 -name: TRITON -def: "ThermoFinnigan TRITON MS." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000199 -name: TSQ Quantum -def: "ThermoFinnigan TSQ Quantum MS." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000200 -name: ultima -def: "IonSpec Ultima MS." [PSI:MS] -is_a: MS:1000123 ! IonSpec instrument model - -[Term] -id: MS:1000201 -name: ultraflex -def: "Bruker Daltonics' ultraflex: MALDI TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1000202 -name: ultraflex TOF/TOF -def: "Bruker Daltonics' ultraflex TOF/TOF: MALDI TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1000203 -name: Voyager-DE PRO -def: "Applied Biosystems/MDS SCIEX Voyager-DE PRO MS." [PSI:MS] -is_a: MS:1000495 ! Applied Biosystems instrument model - -[Term] -id: MS:1000204 -name: Voyager-DE STR -def: "Applied Biosystems/MDS SCIEX Voyager-DE STR MS." [PSI:MS] -is_a: MS:1000495 ! Applied Biosystems instrument model - -[Term] -id: MS:1000205 -name: selected ion monitoring -def: "The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum." [PSI:MS] -synonym: "MIM" RELATED [] -synonym: "Multiple Ion Monitoring" EXACT [] -synonym: "SIM" EXACT [] -is_a: MS:1000596 ! measurement method - -[Term] -id: MS:1000206 -name: selected reaction monitoring -def: "Data acquired from specific product ions corresponding to m/z selected precursor ions recorded via multiple stages of mass spectrometry. Selected reaction monitoring can be performed in time or in space." [PSI:MS] -synonym: "MRM" RELATED [] -synonym: "Multiple Reaction Monitoring" RELATED [] -synonym: "SRM" EXACT [] -is_a: MS:1000596 ! measurement method - -[Term] -id: MS:1000207 -name: accurate mass -def: "OBSOLETE An experimentally determined mass that is can be to determine a unique elemental formula. For ions less than 200 u, a measurement with 5 ppm accuracy is sufficient to determine the elemental composition." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -comment: This child of the former purgatory term ion attribute was made obsolete. -relationship: has_units UO:0000002 ! mass unit -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000208 -name: average mass -def: "OBSOLETE The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -comment: This child of the former purgatory term ion attribute was made obsolete. -relationship: has_units UO:0000002 ! mass unit -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000209 -name: appearance energy -def: "OBSOLETE The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended." [PSI:MS] -synonym: "AE" EXACT [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -comment: This child of the former purgatory term ion attribute was made obsolete. -relationship: has_units UO:0000266 ! electronvolt -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000210 -name: base peak -def: "The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures." [PSI:MS] -synonym: "BP" EXACT [] -is_a: MS:1000231 ! peak - -[Term] -id: MS:1000211 -name: OBSOLETE charge number -def: "OBSOLETE The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_obsolete: true -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1000212 -name: dalton -def: "OBSOLETE A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg." [PSI:MS] -comment: This term was made obsolete because it was redundant with the Unit Ontology term dalton (UO:0000221). -is_obsolete: true - -[Term] -id: MS:1000213 -name: electron affinity -def: "OBSOLETE The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy." [PSI:MS] -comment: This child of the former purgatory term ion attribute was made obsolete. -synonym: "EA" EXACT [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000214 -name: electron energy obsolete -def: "OBSOLETE The potential difference through which electrons are accelerated before they are used to bring about electron ionization." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000215 -name: exact mass -def: "OBSOLETE The calculated mass of an ion or molecule containing a single isotope of each atom." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -comment: This child of the former purgatory term ion attribute was made obsolete. -relationship: has_units UO:0000002 ! mass unit -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000216 -name: field-free region -def: "A section of a mass spectrometer in which there are no electric or magnetic fields." [PSI:MS] -synonym: "FFR" EXACT [] -is_a: MS:1000487 ! ion optics attribute - -[Term] -id: MS:1000217 -name: ionization cross section -def: "OBSOLETE A measure of the probability that a given ionization process will occur when an atom or molecule interacts with a photon, electron, atom or molecule." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000218 -name: ionization efficiency -def: "OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS] -comment: This term was made obsolete because it was replaced by ionization efficiency (MS:1000392). -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000219 -name: ionization energy -def: "OBSOLETE The minimum energy required to remove an electron from an atom or molecule to produce a positive ion." [PSI:MS] -synonym: "IE" EXACT [] -comment: This child of the former purgatory term ion attribute was made obsolete. -xref: value-type:xsd\:float "The allowed value-type for this CV term." -relationship: has_units UO:0000266 ! electronvolt -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000220 -name: isotope dilution mass spectrometry -def: "OBSOLETE A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard." [PSI:MS] -comment: This child of the former purgatory term mass spectrometry was made obsolete. -synonym: "IDMS" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000221 -name: magnetic deflection -def: "The deflection of charged particles in a magnetic field due to a force equal to qvxB where q is the particle charge, v its velocity and B the magnetic field. Magnetic deflection of an ion beam is used for m/z separation in a magnetic sector mass spectrometer." [PSI:MS] -is_a: MS:1000597 ! ion optics type - -[Term] -id: MS:1000222 -name: mass defect -def: "OBSOLETE The difference between the monoisotopic and nominal mass of a molecule or atom." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -comment: This child of the former purgatory term ion attribute was made obsolete. -relationship: has_units UO:0000002 ! mass unit -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000223 -name: mass number -def: "OBSOLETE The sum of the protons and neutrons in an atom, molecule or ion." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -comment: This child of the former purgatory term ion attribute was made obsolete. -is_obsolete: true -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1000224 -name: molecular mass -def: "Mass of a molecule measured in unified atomic mass units (u or Da)." [https://en.wikipedia.org/wiki/Molecular_mass] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000861 ! molecular entity property -relationship: has_units UO:0000002 ! mass unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000225 -name: monoisotopic mass -def: "OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -comment: This child of the former purgatory term ion attribute was made obsolete. -relationship: has_units UO:0000002 ! mass unit -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000226 -name: molecular beam mass spectrometry -def: "OBSOLETE A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -synonym: "MBMS" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000227 -name: multiphoton ionization -def: "Photoionization of an atom or molecule in which in two or more photons are absorbed." [PSI:MS] -synonym: "MPI" EXACT [] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000228 -name: nitrogen rule -def: "OBSOLETE An organic molecule containing the elements C, H, O, S, P, or halogen has an odd nominal mass if it contains an odd number of nitrogen atoms." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000229 -name: nominal mass -def: "OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer value." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -comment: This child of the former purgatory term ion attribute was made obsolete. -relationship: has_units UO:0000002 ! mass unit -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000230 -name: odd-electron rule -def: "OBSOLETE Odd-electron ions may dissociate to form either odd or even-electron ions, whereas even-electron ions generally form even-electron fragment ions." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000231 -name: peak -def: "A localized region of relatively large ion signal in a mass spectrum. Although peaks are often associated with particular ions, the terms peak and ion should not be used interchangeably." [PSI:MS] -relationship: part_of MS:1000442 ! spectrum - -[Term] -id: MS:1000232 -name: peak intensity -def: "OBSOLETE The height or area of a peak in a mass spectrum." [PSI:MS] -comment: This term was made obsolete because it was replaced by base peak intensity (MS:1000505). -is_obsolete: true - -[Term] -id: MS:1000233 -name: proton affinity -def: "OBSOLETE The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states." [PSI:MS] -synonym: "PA" EXACT [PSI:MS] -comment: This child of the former purgatory term ion attribute was made obsolete. -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000234 -name: mass resolving power -def: "OBSOLETE In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported." [PSI:MS] -comment: This term was made obsolete because it was replaced by mass resolving power (MS:1000800). -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000235 -name: total ion current chromatogram -def: "Representation of the total ion current detected in each of a series of mass spectra versus time." [PSI:MS] -synonym: "TIC chromatogram" EXACT [] -is_a: MS:1000810 ! ion current chromatogram - -[Term] -id: MS:1000236 -name: transmission -def: "The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000496 ! instrument attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000237 -name: unified atomic mass unit -def: "OBSOLETE A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg." [PSI:MS] -comment: This term was made obsolete because it was redundant with Unit Ontology dalton (UO:0000221). -synonym: "u" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000238 -name: accelerator mass spectrometry -def: "OBSOLETE A mass spectrometry technique in which atoms extracted from a sample are ionized, accelerated to MeV energies and separated according to their momentum, charge and energy." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -synonym: "AMS" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000239 -name: atmospheric pressure matrix-assisted laser desorption ionization -def: "Matrix-assisted laser desorption ionization in which the sample target is at atmospheric pressure and the ions formed by the pulsed laser are sampled through a small aperture into the mass spectrometer." [PSI:MS] -synonym: "AP MALDI" EXACT [] -is_a: MS:1000240 ! atmospheric pressure ionization - -[Term] -id: MS:1000240 -name: atmospheric pressure ionization -def: "Any ionization process in which ions are formed in the gas phase at atmospheric pressure." [PSI:MS] -synonym: "API" EXACT [] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000241 -name: Atmostpheric Pressure Photoionization -def: "OBSOLETE Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization." [PSI:MS] -comment: This term was made obsolete because it was replaced by atmospheric pressure photoionization (MS:1000382). -synonym: "APPI" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000242 -name: blackbody infrared radiative dissociation -def: "A special case of infrared multiphoton dissociation wherein excitation of the reactant ion is caused by absorption of infrared photons radiating from heated blackbody surroundings, which are usually the walls of a vacuum chamber. See also infrared multiphoton dissociation." [PSI:MS] -synonym: "BIRD" EXACT [] -is_a: MS:1000044 ! dissociation method - -[Term] -id: MS:1000243 -name: charge-remote fragmentation -def: "OBSOLETE A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -synonym: "CRF" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000244 -name: consecutive reaction monitoring -def: "OBSOLETE MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS] -comment: This former purgatory term was made obsolete. -synonym: "CRM" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000245 -name: charge stripping -def: "The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion." [PSI:MS] -synonym: "CS" EXACT [] -is_a: MS:1000510 ! precursor activation attribute - -[Term] -id: MS:1000246 -name: delayed extraction -def: "The application of the accelerating voltage pulse after a time delay in desorption ionization from a surface. The extraction delay can produce energy focusing in a time-of-flight mass spectrometer." [PSI:MS] -synonym: "DE" EXACT [] -is_a: MS:1000597 ! ion optics type - -[Term] -id: MS:1000247 -name: desorption ionization -def: "The formation of ions from a solid or liquid material after the rapid vaporization of that sample." [PSI:MS] -synonym: "DI" EXACT [] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000248 -name: direct insertion probe -def: "A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization." [PSI:MS] -synonym: "DIP" EXACT [] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000249 -name: direct liquid introduction -def: "The delivery of a liquid sample into a mass spectrometer for spray or desorption ionization." [PSI:MS] -synonym: "DLI" EXACT [] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000250 -name: electron capture dissociation -def: "A process in which a multiply protonated molecules interacts with a low energy electrons. Capture of the electron leads the liberation of energy and a reduction in charge state of the ion with the production of the (M + nH) (n-1)+ odd electron ion, which readily fragments." [PSI:MS] -synonym: "ECD" EXACT [] -is_a: MS:1000044 ! dissociation method - -[Term] -id: MS:1000251 -name: even-electron ion -def: "OBSOLETE An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -synonym: "EE" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000252 -name: electron-induced excitation in organics -def: "OBSOLETE The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -synonym: "EIEIO" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000253 -name: electron multiplier -def: "A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. The secondary electrons are then accelerated to other electrodes or parts of a continuous electrode to produce further secondary electrons." [PSI:MS] -synonym: "EM" EXACT [] -is_a: MS:1000026 ! detector type - -[Term] -id: MS:1000254 -name: electrostatic energy analyzer -def: "A device consisting of conducting parallel plates, concentric cylinders or concentric spheres that separates charged particles according to their kinetic energy by means of an electric field that is constant in time." [PSI:MS] -synonym: "ESA" EXACT [] -is_a: MS:1000443 ! mass analyzer type - -[Term] -id: MS:1000255 -name: flowing afterglow -def: "An ion source immersed in a flow of helium or other inert buffer gas that carries the ions through a meter-long reactor at pressures around 100 Pa." [PSI:MS] -synonym: "FA" EXACT [] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000256 -name: high-field asymmetric waveform ion mobility spectrometry -def: "OBSOLETE The separation of ions between two concentric cylindrical electrodes due to application of a high voltage asymmetric waveform whereby ions migrate towards one of the two electrodes depending on the ratio of the high- to low-field mobility of the ion." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -synonym: "FAIMS" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000257 -name: field desorption -def: "The formation of gas-phase ions from a material deposited on a solid surface in the presence of a high electric field. Because this process may encompass ionization by field ionization or other mechanisms, it is not recommended as a synonym for field desorption ionization." [PSI:MS] -synonym: "FD" EXACT [] -is_a: MS:1000247 ! desorption ionization - -[Term] -id: MS:1000258 -name: field ionization -def: "The removal of electrons from any species by interaction with a high electric field." [PSI:MS] -synonym: "FI" EXACT [] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000259 -name: glow discharge ionization -def: "The formation of ions in the gas phase and from solid samples at the cathode by application of a voltage to a low pressure gas." [PSI:MS] -synonym: "GD-MS" EXACT [] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000260 -name: ion kinetic energy spectrometry -def: "OBSOLETE A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -synonym: "IKES" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000261 -name: ion mobility spectrometry -def: "OBSOLETE The separation of ions according to their velocity through a buffer gas under the influence of an electric field." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -synonym: "IMS" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000262 -name: infrared multiphoton dissociation -def: "Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons." [PSI:MS] -synonym: "IRMPD" EXACT [] -is_a: MS:1000044 ! dissociation method - -[Term] -id: MS:1000263 -name: isotope ratio mass spectrometry -def: "OBSOLETE The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer." [PSI:MS] -comment: This child of the former purgatory term mass spectrometry was made obsolete. -synonym: "IRMS" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000264 -name: ion trap -def: "A device for spatially confining ions using electric and magnetic fields alone or in combination." [PSI:MS] -synonym: "IT" EXACT [] -is_a: MS:1000443 ! mass analyzer type - -[Term] -id: MS:1000265 -name: kinetic energy release distribution -def: "OBSOLETE Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -synonym: "KERD" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000266 -name: Laser Desorption -def: "OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules." [PSI:MS] -comment: This term was made obsolete because it was replaced by laser desorption ionization (MS:1000393). -synonym: "Laser Ionization MERGE" EXACT [] -synonym: "LD" EXACT [] -is_obsolete: true -replaced_by: MS:1000393 - -[Term] -id: MS:1000267 -name: mass analyzed ion kinetic energy spectrometry -def: "OBSOLETE Spectra that are obtained from a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector in reverse geometry. The accelerating voltage, V, and the magnetic sector field, B, are set at fixed values to select the precursor ions, which are then allowed to dissociate or to react in a field free region between the two sectors. The kinetic energy product ions of m/z selected precursor ions is analyzed by scanning the electric sector field, E. The width of the product ion spectrum peaks is related to the kinetic energy release distribution (KERD) for the dissociation process." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -synonym: "MIKES" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000268 -name: mass spectrometry -def: "OBSOLETE The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments." [PSI:MS] -comment: This former purgatory term was made obsolete. -synonym: "MS" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000269 -name: mass spectrometry/mass spectrometry -def: "OBSOLETE The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -synonym: "MS/MS" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000270 -name: multiple stage mass spectrometry -def: "OBSOLETE Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions." [PSI:MS] -comment: This child of the former purgatory term m/z Separation Method was made obsolete. -synonym: "MSn" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000271 -name: Negative Ion chemical ionization -def: "Chemical ionization that results in the formation of negative ions." [PSI:MS] -synonym: "NICI" EXACT [] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000272 -name: neutralization reionization mass spectrometry -def: "With this technique, m/z selected ions form neutrals by charge transfer to a collision gas or by dissociation. The neutrals are separated from the remaining ions and ionized in collisions with a second gas. This method is used to investigate reaction intermediates and other unstable species." [PSI:MS] -synonym: "NRMS" EXACT [] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000273 -name: photoionization -def: "The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended." [PSI:MS] -synonym: "PI" EXACT [] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000274 -name: pyrolysis mass spectrometry -def: "A mass spectrometry technique in which the sample is heated to the point of decomposition and the gaseous decomposition products are introduced into the ion source." [PSI:MS] -synonym: "PyMS" EXACT [] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000275 -name: collision quadrupole -def: "A transmission quadrupole to which an oscillating potential is applied so as to focus a beam of ions through a collision gas with no m/z separation." [PSI:MS] -synonym: "q" EXACT [] -is_a: MS:1000597 ! ion optics type - -[Term] -id: MS:1000276 -name: resonance enhanced multiphoton ionization -def: "Multiphoton ionization in which the ionization cross section is significantly enhanced because the energy of the incident photons is resonant with an intermediate excited state of the neutral species." [PSI:MS] -synonym: "REMPI" EXACT [] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000277 -name: residual gas analyzer -def: "OBSOLETE A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -synonym: "RGA" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000278 -name: surface enhanced laser desorption ionization -def: "The formation of ionized species in the gas phase from analytes deposited on a particular surface substrate which is irradiated with a laser beam of which wavelength is absorbed by the surface. See also desorption/ionization on silicon and laser desorption/ionization." [PSI:MS] -synonym: "SELDI" EXACT [] -is_a: MS:1000406 ! surface ionization - -[Term] -id: MS:1000279 -name: surface enhanced neat desorption -def: "Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface." [PSI:MS] -synonym: "SEND" EXACT [] -is_a: MS:1000406 ! surface ionization - -[Term] -id: MS:1000280 -name: suface ionization -def: "OBSOLETE The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature." [PSI:MS] -comment: This term was made obsolete because it was replaced by surface ionization (MS:1000406). -synonym: "SI" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000281 -name: selected ion flow tube -def: "A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions." [PSI:MS] -synonym: "SIFT" EXACT [] -is_a: MS:1000597 ! ion optics type - -[Term] -id: MS:1000282 -name: sustained off-resonance irradiation -def: "A technique associated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to carry out ion/neutral reactions such as low-energy collision-induced dissociation. A radio-frequency electric field of slightly off-resonance to the cyclotron frequency of the reactant ion cyclically accelerates and decelerates the reactant ion that is confined in the Penning ion trap. The ion's orbit does not exceed the dimensions of ion trap while the ion undergoes an ion/neutral species process that produces a high average translational energy for an extended time." [PSI:MS] -synonym: "SORI" EXACT [] -is_a: MS:1000044 ! dissociation method - -[Term] -id: MS:1000283 -name: Spark Source Mass Spectrometry -def: "OBSOLETE Mass spectrometry using spark ionization." [PSI:MS] -comment: This term was made obsolete because it was replaced by spark ionization (MS:1000404). -synonym: "SSMS" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000284 -name: stored waveform inverse fourier transform -def: "A technique to create excitation waveforms for ions in FT-ICR mass spectrometer or Paul ion trap. An excitation waveform in the time-domain is generated by taking the inverse Fourier transform of an appropriate frequency-domain programmed excitation spectrum, in which the resonance frequencies of ions to be excited are included. This technique may be used for selection of precursor ions in MS2 experiments." [PSI:MS] -synonym: "SWIFT" EXACT [] -is_a: MS:1000443 ! mass analyzer type - -[Term] -id: MS:1000285 -name: total ion current -def: "The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum." [PSI:MS] -synonym: "TIC" EXACT [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1003058 ! spectrum property -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000286 -name: time lag focusing -def: "Energy focusing in a time-of-flight mass spectrometer that is accomplished by introducing a time delay between the formation of the ions and the application of the accelerating voltage pulse." [PSI:MS] -synonym: "TLF" EXACT [] -is_a: MS:1000597 ! ion optics type - -[Term] -id: MS:1000287 -name: time-of-flight mass spectrometer -def: "OBSOLETE An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -synonym: "TOF-MS" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000288 -name: cyclotron -def: "A device that uses an oscillating electric field and magnetic field to accelerate charged particles." [PSI:MS] -is_a: MS:1000443 ! mass analyzer type - -[Term] -id: MS:1000289 -name: double-focusing mass spectrometer -def: "OBSOLETE A mass spectrometer that uses a magnetic sector for m/z focusing and an electric sector for energy focusing of an ion beam." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000290 -name: hybrid mass spectrometer -def: "OBSOLETE A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000291 -name: linear ion trap -def: "A two dimensional Paul ion trap in which ions are confined in the axial dimension by means of an electric field at the ends of the trap." [PSI:MS] -is_a: MS:1000264 ! ion trap - -[Term] -id: MS:1000292 -name: mass spectrograph obsolete -def: "OBSOLETE An instrument that separates a beam of ions according to their mass-to-charge ratio in which the ions are directed onto a focal plane detector such as a photographic plate." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000293 -name: mass spectrometer -def: "OBSOLETE An instrument that measures the mass-to-charge ratio and relative abundances of ions." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000294 -name: mass spectrum -def: "A plot of the relative abundance of a beam or other collection of ions as a function of the mass-to-charge ratio (m/z)." [PSI:MS] -is_a: MS:1000524 ! data file content -is_a: MS:1000559 ! spectrum type - -[Term] -id: MS:1000295 -name: mattauch-herzog geometry -def: "OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/(4 ?(2)) radians in a radial electric field is followed by a magnetic deflection of ?/2 radians." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000296 -name: nier-johnson geometry -def: "OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/2 radians in a radial electric field analyzer is followed by a magnetic deflection of ?/3 radians." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000297 -name: paul ion trap -def: "OBSOLETE A device that permits the trapping of ions by means of an alternating current voltage. The ejection of ions with a m/z less than a prescribed value and retention of those with higher mass depends on the application of radio frequency voltages between a ring electrode and two end-cap electrodes to confine the ions in a circular path. The choice of these voltages determines the m/z below which ions are ejected." [PSI:MS] -comment: This term was made obsolete because it is redundant to quadrupole ion trap. -synonym: "quadrupole ion trap" RELATED [] -is_obsolete: true - -[Term] -id: MS:1000298 -name: prolate traochoidal mass spectrometer -def: "OBSOLETE A mass spectrometer in which the ions of different m/z are separated by means of crossed electric and magnetic fields in such a way that the selected ions follow a prolate trochoidal path." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000299 -name: quistor -def: "OBSOLETE An abbreviation of quadrupole ion storage trap. This term is synonymous with Paul Ion Trap. If so then add a synonym to paul and obsolete this term." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000300 -name: reflectron -def: "A time-of-flight mass spectrometer that uses a static electric field to reverse the direction of travel of the ions entering it. A reflectron improves mass resolution by assuring that ions of the same m/z but different kinetic energy arrive at the detector at the same time." [PSI:MS] -is_a: MS:1000597 ! ion optics type - -[Term] -id: MS:1000301 -name: sector mass spectrometer -def: "OBSOLETE A mass spectrometer consisting of one or more magnetic sectors for m/z selection in a beam of ions. Such instruments may also have one or more electric sectors for energy selection." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000302 -name: tandem mass spectrometer -def: "OBSOLETE A mass spectrometer designed for mass spectrometry/mass spectrometry." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000303 -name: transmission quadrupole mass spectrometer -def: "OBSOLETE A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000304 -name: accelerating voltage -def: "The electrical potential used to impart kinetic energy to ions in a mass spectrometer." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000487 ! ion optics attribute -relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000305 -name: cyclotron motion -def: "OBSOLETE The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB." [PSI:MS] -comment: This child of the former purgatory term m/z Separation Method was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000306 -name: dynamic mass spectrometry -def: "OBSOLETE A mass spectrometer in which m/z separation using one or more electric fields that vary with time." [PSI:MS] -comment: This child of the former purgatory term mass spectrometer was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000307 -name: einzel lens -def: "Three element charged particle lens in which the first and third elements are held at the same voltage. Such a lens produces focusing without changing the translational energy of the particle." [PSI:MS] -is_a: MS:1000597 ! ion optics type - -[Term] -id: MS:1000308 -name: electric field strength -def: "The magnitude of the force per unit charge at a given point in space." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000487 ! ion optics attribute -relationship: has_units UO:0000268 ! volt per meter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000309 -name: first stability region -def: "The region of a Mathieu stability diagram closest to the origin. Ions within this region can traverse the full length of a transmission quadrupole." [PSI:MS] -is_a: MS:1000597 ! ion optics type - -[Term] -id: MS:1000310 -name: fringing field -def: "The electric or magnetic field that extends from the edge of a sector, lens or other ion optics element." [PSI:MS] -is_a: MS:1000597 ! ion optics type - -[Term] -id: MS:1000311 -name: kinetic energy analyzer -def: "A device for measuring the kinetic energy of charged particles using a retarding field, time-of-flight, or the extent of deflection in an electric or magnetic field." [PSI:MS] -is_a: MS:1000597 ! ion optics type - -[Term] -id: MS:1000312 -name: mass limit -def: "OBSOLETE The m/z value above which ions cannot be detected in a mass spectrometer." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000313 -name: scan m/z range? -def: "OBSOLETE The limit of m/z over which a mass spectrometer can detect ions." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000314 -name: mass selective axial ejection -def: "OBSOLETE The use of mass selective instability to eject ions of selected m/z values from an ion trap." [PSI:MS] -comment: This child of the former purgatory term m/z Separation Method was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000315 -name: mass selective instability -def: "OBSOLETE A method for selective ejection of ions according to their m/z value in an ion trap." [PSI:MS] -comment: This child of the former purgatory term m/z Separation Method was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000316 -name: mathieu stability diagram -def: "OBSOLETE A graphical representation expressed in terms of reduced coordinates that describes charged particle motion in a quadrupole mass filter or quadrupole ion trap mass spectrometer." [PSI:MS] -comment: This child of the former purgatory term m/z Separation Method was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000317 -name: orthogonal extraction -def: "OBSOLETE The pulsed acceleration of ions perpendicular to their direction of travel into a time-of-flight mass spectrometer. Ions may be extracted from a directional ion source, drift tube or m/z separation stage." [PSI:MS] -comment: This child of the former purgatory term m/z Separation Method was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000318 -name: resonance ion ejection -def: "OBSOLETE A mode of ion ejection in a quadrupole ion trap that relies on a auxiliary radio frequency voltage that is applied to the end-cap electrodes. The voltage is tuned to the secular frequency of a particular ion to eject it." [PSI:MS] -comment: This child of the former purgatory term m/z Separation Method was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000319 -name: space charge effect -def: "The mutual repulsion of particles of like charge that limits the current in a charged-particle beam and causes beams or packets of charged particles to expand radially over time." [PSI:MS] -is_a: MS:1000487 ! ion optics attribute - -[Term] -id: MS:1000320 -name: static field -def: "An electric or magnetic field that does not change in time." [PSI:MS] -is_a: MS:1000597 ! ion optics type - -[Term] -id: MS:1000321 -name: 2E Mass Spectrum -def: "OBSOLETE A mass spectrum obtained by setting the electric sector field E to twice the value required to transmit the main ion-beam thereby allowing ions with a kinetic energy-to-charge ratio twice that of the main ion-beam to be transmitted. Product ions resulting from partial charge transfer reactions such as m^2+ + N ? m^+ + N^+ that occur in a collision cell (containing a gas, N) located in a field-free region preceding a magnetic and electric sector combination are detected. When the magnetic sector field B is scanned, a mass spectrum of singly charged product ions of doubly charged precursor ions is obtained." [PSI:MS] -comment: This child of the former purgatory term m/z Separation Method was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000322 -name: charge inversion mass spectrum -def: "The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z." [PSI:MS] -is_a: MS:1000294 ! mass spectrum - -[Term] -id: MS:1000323 -name: constant neutral loss scan -def: "OBSOLETE Spectrum of all precursor ions that undergo a selected m/z decrement." [PSI:MS] -comment: This former purgatory term was made obsolete. -synonym: "constant neutral mass loss scan" RELATED [] -synonym: "fixed neutral fragment scan" RELATED [] -is_obsolete: true - -[Term] -id: MS:1000324 -name: constant neutral gain scan -def: "OBSOLETE Spectrum of all precursor ions that undergo a selected m/z increment." [PSI:MS] -comment: This former purgatory term was made obsolete. -synonym: "Constant Neutral Mass Gain Scan" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000325 -name: constant neutral gain spectrum -def: "A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell." [PSI:MS] -synonym: "constant neutral mass gain spectrum" EXACT [] -is_a: MS:1000294 ! mass spectrum - -[Term] -id: MS:1000326 -name: constant neutral loss spectrum -def: "A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum." [PSI:MS] -synonym: "constant neutral mass loss spectrum" EXACT [] -is_a: MS:1000294 ! mass spectrum - -[Term] -id: MS:1000327 -name: consecutive reaction monitoring -def: "OBSOLETE A type of MS2 experiments with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS] -comment: This term was made obsolete because it was replaced by consecutive reaction monitoring (MS:1000244). -is_obsolete: true - -[Term] -id: MS:1000328 -name: e/2 mass spectrum -def: "A mass spectrum obtained using a sector mass spectrometer in which the electric sector field E is set to half the value required to transmit the main ion-beam. This spectrum records the signal from doubly charged product ions of charge-stripping reactions." [PSI:MS] -is_a: MS:1000294 ! mass spectrum - -[Term] -id: MS:1000329 -name: linked scan -def: "OBSOLETE A scan in an instrument with two or more m/z analysers or in a sector mass spectrometer that incorporates at least one magnetic sector and one electric sector. Two or more of the analyzers are scanned simultaneously so as to preserve a predetermined relationship between scan parameters to produce a product ion, precursor ion or constant neutral loss spectrum." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000330 -name: linked scan at constant b/e -def: "OBSOLETE A linked scan at constant B/E may be performed on a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector. The magnetic field B and the electric field E are scanned simultaneously while the accelerating voltage V is held constant, so as to maintain the ratio of the two fields constant. This linked scan may record a product ion spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors." [PSI:MS] -comment: This child of the former purgatory term linked scan was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000331 -name: Linked Scan at Constant E2/V -def: "OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector. The electric sector field, E, and the accelerating voltage, V, are scanned simultaneously, so as to maintain the ratio E2/V at a constant value. This linked scan recordss a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors." [PSI:MS] -comment: This child of the former purgatory term linked scan was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000332 -name: Linked Scan at Constant B2/E -def: "OBSOLETE A linked scan performed on a sector mass spectrometer that incorporates at least one electric sector plus one magnetic sector in either order. The accelerating voltage is fixed and the magnetic field, B, and the electric field, E, are scanned simultaneously so as to maintain the ratio B2/E at a constant value. This linked scan records a precursor ion spectrum of dissociation or other reactions occurring in the field free region preceding the two sectors. The term B2/E linked scan is not recommended." [PSI:MS] -comment: This child of the former purgatory term linked scan was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000333 -name: Linked Scan at Constant B[1-(E/E0)]^1/2 / E -def: "OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector placed in either order. The accelerating voltage is fixed while scanning the magnetic field, B, and electric field, E, simultaneously, so as to maintain the quantity B[1-(E/E0)]1/2/E at a constant value. This linked scan records a constant neutral mass loss (or gain) spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. E0 is the electric field required to transmit the singly charged analog of the desired neutral fragment. The term B[1-(E/E0)]1/2/E linked scan." [PSI:MS] -comment: This child of the former purgatory term linked scan was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000334 -name: MS/MS in Time -def: "OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in a single m/z analyzer (such as a Paul Ion Trap or FTMS) in discreet steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time." [PSI:MS] -comment: This child of the former purgatory term m/z Separation Method was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000335 -name: MS/MS in Space -def: "OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in m/z analyzers separated in space. Specific m/z separation functions are designed such that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyser for m/z separation and data acquisition." [PSI:MS] -comment: This child of the former purgatory term m/z Separation Method was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000336 -name: neutral loss -def: "The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID: 21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type)." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001055 ! modification parameters -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000337 -name: nth generation product ion -def: "OBSOLETE Serial product ions from dissociation of selected precursor ions where n refers to the number of stages of dissociation. The term granddaughter ion is deprecated." [PSI:MS] -comment: This child of the former purgatory term product ion was made obsolete. -synonym: "granddaughter ion" RELATED [] -is_obsolete: true - -[Term] -id: MS:1000338 -name: nth generation product ion scan -def: "OBSOLETE The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000339 -name: nth generation product ion spectrum -def: "OBSOLETE The mass spectrum recorded from any mass spectrometer in which the appropriate scan function can be set to record the appropriate generation product ion or ions of m/z selected precursor ions." [PSI:MS] -comment: This term was made obsolete because it was merged with MSn spectrum (MS:1000580). -is_obsolete: true - -[Term] -id: MS:1000340 -name: precursor ion -def: "OBSOLETE An ion that reacts to form particular product ions. The reaction can be unimolecular dissociation, ion/molecule reaction, isomerization, or change in charge state. The term parent ion is deprecated." [PSI:MS] -comment: This child of the former purgatory term ion role was made obsolete. -synonym: "parent ion" RELATED [] -is_obsolete: true - -[Term] -id: MS:1000341 -name: precursor ion spectrum -def: "Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z." [PSI:MS] -is_a: MS:1000294 ! mass spectrum - -[Term] -id: MS:1000342 -name: product ion -def: "OBSOLETE An ion formed as the product of a reaction involving a particular precursor ion. The reaction can be unimolecular dissociation to form fragment ions, an ion/molecule reaction, or simply involve a change in the number of charges. The term fragment ion is deprecated. The term daughter ion is deprecated." [PSI:MS] -comment: This child of the former purgatory term ion role was made obsolete. -synonym: "daughter ion" RELATED [] -is_obsolete: true - -[Term] -id: MS:1000343 -name: product ion spectrum -def: "OBSOLETE A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions." [PSI:MS] -comment: This term was made obsolete because it was merged with MSn spectrum (MS:1000580). -is_a: MS:1000294 ! mass spectrum -is_obsolete: true - -[Term] -id: MS:1000344 -name: progeny ion -def: "OBSOLETE A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ -> M2+ -> M3+ -> M4+ -> M5+. M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -synonym: "Progeny Fragment Ion" EXACT [] -is_obsolete: true - -[Term] -id: MS:1000345 -name: array detector -def: "Detector comprising several ion collection elements, arranged in a line or grid where each element is an individual detector." [PSI:MS] -is_a: MS:1000026 ! detector type - -[Term] -id: MS:1000346 -name: conversion dynode -def: "A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected." [PSI:MS] -is_a: MS:1000026 ! detector type - -[Term] -id: MS:1000347 -name: dynode -def: "One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode." [PSI:MS] -is_a: MS:1000026 ! detector type - -[Term] -id: MS:1000348 -name: focal plane collector -def: "A detector for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane." [PSI:MS] -is_a: MS:1000026 ! detector type - -[Term] -id: MS:1000349 -name: ion-to-photon detector -def: "A detector in which ions strike a conversion dynode to produce electrons that in turn strike a phosphor and the resulting photons are detected by a photomultiplier." [PSI:MS] -is_a: MS:1000026 ! detector type - -[Term] -id: MS:1000350 -name: point collector -def: "A detector in which the ion beam is focused onto a point and the individual ions arrive sequentially." [PSI:MS] -is_a: MS:1000026 ! detector type - -[Term] -id: MS:1000351 -name: postacceleration detector -def: "A detector in which the charged particles are accelerated to a high velocity and impinge on a conversion dynode, emitting secondary electrons. The electrons are accelerated onto a phosphor screen, which emits photons that are in turn detected using a photomultiplier or other photon detector." [PSI:MS] -is_a: MS:1000026 ! detector type - -[Term] -id: MS:1000352 -name: secondary electron -def: "OBSOLETE Electrons that are ejected from a sample surface as a result of bombardment by a primary beam of atoms, ions or photons. WAS IN DETECTOR TYPE. Where should it go." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000353 -name: adduct ion -def: "Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules." [PSI:MS] -is_a: MS:1003055 ! adduct - -[Term] -id: MS:1000354 -name: aromatic ion -def: "OBSOLETE A planar cyclic ion that obeys the Hueckel (4n + 2) rule where n is a positive integer representing the number of conjugated Pi electrons. Charge delocalization leads to greater stability compared to a hypothetical localized structure." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000355 -name: analog ion -def: "OBSOLETE Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000356 -name: anti-aromatic ion -def: "OBSOLETE A planar cyclic ion with 4n ? electrons and is therefore not aromatic." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000357 -name: cationized molecule -def: "OBSOLETE An ion formed by the association of a cation with a neutral molecule, M, for example [M+ Na]+ and [M + K]+. The terms quasi-molecular ion and pseudo-molecular ion should not be used." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000358 -name: cluster ion -def: "OBSOLETE An ion formed by a multi-component atomic or molecular assembly of one or more ions with atoms or molecules, such as [(H20)nH]+, [(NaCl)nNa]+ and [(H3PO3)nHPO3]-." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000359 -name: Conventional ion -def: "OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin are both formally located in the same atom or group of atoms, as opposed to the spatially separate electronic configuration of distonic ions. The radical cation of methanol, CH3OH+, in which the charge and spin sites are formally located at the O atom is an example of a conventional ion, whereas .CH2-OH2+ is a distonic ion." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000360 -name: diagnostic ion -def: "OBSOLETE A product ion whose formation reveals structural or compositional information of its precursor. For instance, the phenyl cation in an electron ionization mass spectrum is a diagnostic ion for benzene and derivatives." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000361 -name: dimeric ion -def: "OBSOLETE An ion formed by ionization of a dimer or by the association of an ion with its neutral counterpart such as [M2]+ or [M-H-M]+." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000362 -name: distonic ion -def: "OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin cannot be both formally located in the same atom or group of atoms as it can be with a conventional ion. For example, CH2-OH2+ is a distonic ion whereas the radical cation of methanol, CH3OH+ is a conventional ion." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000363 -name: enium ion -def: "OBSOLETE A positively charged lower-valency ion of the nonmetallic elements. The methenium ion is CH3+. Other examples are the oxenium, sulfenium, nitrenium, phosphenium, and halenium ions." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000364 -name: fragment ion -def: "OBSOLETE A product ion that results from the dissociation of a precursor ion." [PSI:MS] -comment: This term was made obsolete because it was replaced by product ion (MS:1000342). -is_obsolete: true - -[Term] -id: MS:1000365 -name: ion? -def: "OBSOLETE An atomic or molecular species having a net positive or negative electric charge." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000366 -name: Isotopologue ion -def: "OBSOLETE An ion that differs only in the isotopic composition of one or more of its constituent atoms. For example CH4+ and CH3D+ or 10BF3 and 11BF3. The term isotopologue is a contraction of isotopic homologue." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000367 -name: Isotopomeric ion -def: "OBSOLETE Isomeric ion having the same numbers of each isotopic atom but differing in their positions. Isotopomeric ions can be either configurational isomers in which two atomic isotopes exchange positions or isotopic stereoisomers. The term isotopomer is a shortening of isotopic isomer." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000368 -name: metastable ion -def: "OBSOLETE An ion that is formed with internal energy higher than the threshold for dissociation but with a lifetime great enough to allow it to exit the ion source and enter the mass spectrometer where it dissociates before detection." [PSI:MS] -comment: This child of the former purgatory term ion stability type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000369 -name: molecular ion -def: "OBSOLETE An ion formed by the removal of one or more electrons to form a positive ion or the addition off one or more electrons to form a negative ion." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000370 -name: negative ion -def: "OBSOLETE An atomic or molecular species having a net negative electric charge." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000371 -name: non-classical ion -def: "OBSOLETE Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000372 -name: onium ion -def: "OBSOLETE A positively charged hypervalent ion of the nonmetallic elements. Examples are the methonium ion CH5+, the hydrogenonium ion H3+ and the hydronium ion H3O+. Other examples are the carbonium, oxonium, sulfonium, nitronium, diazonium, phosphonium, and halonium ions. Onium ions are not limited to monopositive ions; multiply-charged onium ions exist such as the gitonic (proximal) oxonium dication H4O2+ and the distonic oxonium dication H2O+-CH2-CH2-OH2+." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000373 -name: principal ion -def: "OBSOLETE Most abundant ion of an isotope cluster, such as the 11B79Br2 81Br+ ion of m/z 250 of the cluster of isotopologue molecular ions of BBr3. The term principal ion has also been used to describe ions that have been artificially isotopically enriched in one or more positions such as CH3 13CH3+ or CH2D2 +, but those are best defined as isotopologue ions." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000374 -name: positive ion -def: "OBSOLETE An atomic or molecular species having a net positive electric charge." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000375 -name: protonated molecule -def: "OBSOLETE An ion formed by interaction of a neutral molecule with a proton and represented by the symbol [M + H]+, where M is the neutral molecule. The term 'protonated molecular ion,' 'quasi-molecular ion' and 'pseudo-molecular ion' are not recommended." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000376 -name: radical ion -def: "OBSOLETE An ion, either a cation or anion, containing unpaired electrons in its ground state. The unpaired electron is denoted by a superscript dot alongside the superscript symbol for charge, such as for the molecular ion of a molecule M, that is, M+. Radical ions with more than one charge and/or more than one unpaired electron are denoted such as M(2+)(2). Unless the positions of the unpaired electron and charge can be associated with specific atoms, superscript charge designation should be placed before the superscript dot designation." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000377 -name: reference ion -def: "OBSOLETE A stable ion whose structure is known with certainty. These ions are usually formed by direct ionization of a neutral molecule of known structure and are used to verify by comparison the structure of an unknown ion." [PSI:MS] -comment: This child of the former purgatory term ion chemical type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000378 -name: stable ion -def: "OBSOLETE An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer." [PSI:MS] -comment: This child of the former purgatory term ion stability type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000379 -name: unstable ion -def: "OBSOLETE An ion with sufficient energy to dissociate within the ion source." [PSI:MS] -comment: This child of the former purgatory term ion stability type was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000380 -name: adiabatic ionization -def: "A process whereby an electron is removed from an atom, ion, or molecule to produce an ion in its lowest energy state." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000381 -name: associative ionization -def: "An ionization process in which two excited atoms or molecules react to form a single positive ion and an electron." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000382 -name: atmospheric pressure photoionization -def: "Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization." [PSI:MS] -is_a: MS:1000240 ! atmospheric pressure ionization - -[Term] -id: MS:1000383 -name: autodetachment -def: "The formation of a neutral when a negative ion in a discrete state with an energy greater than the detachment threshold loses an electron spontaneously without further interaction with an energy source." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000384 -name: autoionization -def: "The formation of an ion when an atom or molecule in a discrete state with an energy greater than the ionization threshold loses an electron spontaneously without further interaction with an energy source." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000385 -name: charge exchange ionization -def: "The interaction of an ion with an atom or molecule in which the charge on the ion is transferred to the neutral without the dissociation of either. Synonymous with charge transfer ionization." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000386 -name: chemi-ionization -def: "The reaction of a neutral molecule with an internally excited molecule to form an ion. Note that this term is not synonymous with chemical ionization." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000387 -name: desorption/ionization on silicon -def: "The formation of ions by laser desorption ionization of a sample deposited on a porous silicon surface." [PSI:MS] -is_a: MS:1000247 ! desorption ionization - -[Term] -id: MS:1000388 -name: dissociative ionization -def: "The reaction of a gas-phase molecule that results in its decomposition to form products, one of which is an ion." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000389 -name: electron ionization -def: "The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000390 -name: ion desolvation -def: "OBSOLETE The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000391 -name: ion-pair formation -def: "OBSOLETE The reaction of a molecule to form both a positive ion and negative ion fragment among the products." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000392 -name: ionization efficiency -def: "The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000482 ! source attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000393 -name: laser desorption ionization -def: "The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material." [PSI:MS] -is_a: MS:1000247 ! desorption ionization - -[Term] -id: MS:1000395 -name: liquid secondary ionization -def: "The ionization of any species by the interaction of a focused beam of ions with a sample that is dissolved in a solvent matrix. See also fast atom bombardment and secondary ionization." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000396 -name: membrane inlet -def: "A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source." [PSI:MS] -is_a: MS:1000007 ! inlet type - -[Term] -id: MS:1000397 -name: microelectrospray -def: "Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanoelectrospray." [PSI:MS] -is_a: MS:1000073 ! electrospray ionization - -[Term] -id: MS:1000398 -name: nanoelectrospray -def: "Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potenial on the tip of the electrospray needle and/or a gas presure to push the sample through the needle. See also electrospray ionization and microelectrospray." [PSI:MS] -synonym: "nanospray" EXACT [] -is_a: MS:1000073 ! electrospray ionization - -[Term] -id: MS:1000399 -name: penning ionization -def: "Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000400 -name: plasma desorption ionization -def: "The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000401 -name: pre-ionization state -def: "OBSOLETE An electronic state capable of undergoing auto-Ionization." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000402 -name: secondary ionization -def: "The process in which ions are ejected from a sample surface as a result of bombardment by a primary beam of atoms or ions." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000403 -name: soft ionization -def: "The formation of gas-phase ions without extensive fragmentation." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000404 -name: spark ionization -def: "The formation of ions from a solid material by an intermittent electrical discharge." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000405 -name: surface-assisted laser desorption ionization -def: "The formation of gas-phase ions from molecules that are deposited on a particular surface substrate that is irradiated with a pulsed laser. See also matrix-assisted laser desorption ionization." [PSI:MS] -is_a: MS:1000247 ! desorption ionization - -[Term] -id: MS:1000406 -name: surface ionization -def: "The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000407 -name: thermal ionization -def: "The ionization of a neutral species through contact with a high temperature surface." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000408 -name: vertical ionization -def: "A process in which an electron is removed from or added to a molecule without a change in the positions of the atoms. The resulting ion is typically in an excited vibrational state." [PSI:MS] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000409 -name: association reaction -def: "OBSOLETE The reaction of an ion with a neutral species in which the reactants combine to form a single ion." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000410 -name: alpha-cleavage -def: "OBSOLETE A homolytic cleavage where the bond fission occurs between at the atom adjacent to the atom at the apparent charge site and an atom removed from the aparent charge site by two bonds." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000411 -name: beta-cleavage -def: "OBSOLETE A homolytic cleavage where the bond fission occurs between at an atom removed from the apparent charge site atom by two bonds and an atom adjacent to that atom and removed from the aparent charge site by three bonds." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000412 -name: buffer gas -def: "An inert gas used for collisional deactivation of internally excited ions." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000510 ! precursor activation attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000413 -name: charge-induced fragmentation -def: "OBSOLETE Fragmentation of an odd electron ion in which the cleaved bond is adjacent to the apparent charge site. Synonymous with charge mediated fragmentation." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000414 -name: charge inversion reaction -def: "OBSOLETE Reaction of an ion with a neutral species in which the charge on the product ion is reversed in sign with respect to the reactant ion." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000415 -name: charge permutation reaction -def: "OBSOLETE The reaction of an ion with a neutral species with a resulting change in the magnitude or sign of the charge on the reactant ion." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000416 -name: charge stripping reaction -def: "OBSOLETE Reaction of a positive ion with a neutral species in which the positive charge on the product ion is greater than that on the reactant ion." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000417 -name: charge transfer reaction -def: "OBSOLETE The reaction of an ion with a neutral species in which some or all of the charge of the reactant ion is transferred to the neutral species." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000418 -name: collisional excitation -def: "OBSOLETE The reaction of an ion with a neutral species in which the translational energy of the collision is converted into internal energy of the ion." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000419 -name: collision gas -def: "An inert gas used for collisional excitation. The term target gas is not recommended." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000510 ! precursor activation attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000420 -name: heterolytic cleavage -def: "OBSOLETE Fragmentation of a molecule or ion in which both electrons forming the single bond that is broken remain on one of the atoms that were originally bonded. This term is synonymous with heterolysis." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -synonym: "heterolysis" RELATED [] -is_obsolete: true - -[Term] -id: MS:1000421 -name: high energy collision -def: "OBSOLETE Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000422 -name: beam-type collision-induced dissociation -def: "A collision-induced dissociation process that occurs in a beam-type collision cell." [PSI:MS] -synonym: "HCD" EXACT [] -is_a: MS:1000133 ! collision-induced dissociation - -[Term] -id: MS:1000423 -name: homolytic cleavage -def: "OBSOLETE Fragmentation of an odd electron ion that results from one of a pair of electrons that form a bond between two atoms moving to form a pair with the odd electron on the atom at the apparent charge site. Fragmentation results in the formation of an even electron ion and a radical. This reaction involves the movement of a single electron and is symbolized by a single-barbed arrow. Synonymous with Homolysis." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -synonym: "homolysis" RELATED [] -is_obsolete: true - -[Term] -id: MS:1000424 -name: hydrogen/deuterium exchange -def: "OBSOLETE Exchange of hydrogen atoms with deuterium atoms in a molecule or pre-formed ion in solution prior to introduction into a mass spectrometer, or by reaction of an ion with a deuterated collision gas inside a mass spectrometer." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000425 -name: ion energy loss spectrum -def: "OBSOLETE A plot of the relative abundance of a beam or other collection of ions as a function their loss of translational energy in reactions with neutral species." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000426 -name: ionizing collision -def: "OBSOLETE The reaction of an ion with a neutral species in which one or more electrons are removed from either the ion or neutral." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000427 -name: ion/molecule reaction -def: "OBSOLETE The reaction of an ion with a neutral molecule. The term ion-molecule reaction is not recommended because the hyphen suggests a single species that is that is both an ion and a molecule." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000428 -name: ion/neutral complex -def: "OBSOLETE A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000429 -name: ion/neutral species reaction -def: "OBSOLETE A process wherein a charged species interacts with a neutral reactant to produce either chemically different species or changes in the internal energy of one or both of the reactants." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000430 -name: ion/neutral species exchange reaction -def: "OBSOLETE In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000431 -name: kinetic method -def: "OBSOLETE An approach to determination of ion thermodynamic quantities by a bracketing procedure in which the relative probabilities of competing ion fragmentations are measured via the relative abundances of the reaction products. The extended kinetic method takes the associated entropy changes into account." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000432 -name: low energy collisions -def: "OBSOLETE A collision between an ion and neutral species with translational energy approximately 1000 eV or lower." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000433 -name: low-energy collision-induced dissociation -def: "A collision-induced dissociation process wherein the precursor ion has the translational energy lower than approximately 1000 eV. This process typically requires multiple collisions and the collisional excitation is cumulative." [PSI:MS] -is_a: MS:1000044 ! dissociation method - -[Term] -id: MS:1000434 -name: McLafferty Rearrangement -def: "OBSOLETE A dissociation reaction triggered by transfer of a hydrogen atom via a 6-member transition state to the formal radical/charge site from a carbon atom four atoms removed from the charge/radical site (the gamma-carbon); subsequent rearrangement of electron density leads to expulsion of an olefin molecule. This term was originally applied to ketone ions where the charge/radical site is the carbonyl oxygen, but it is now more widely applied." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000435 -name: photodissociation -def: "A process wherein the reactant ion is dissociated as a result of absorption of one or more photons." [PSI:MS] -synonym: "multiphoton dissociation" EXACT [] -synonym: "MPD" EXACT [] -is_a: MS:1000044 ! dissociation method - -[Term] -id: MS:1000436 -name: partial charge transfer reaction -def: "OBSOLETE Reaction of an ion with a neutral species in which some but not all of the ion charge is transferred to the neutral." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000437 -name: ion reaction -def: "OBSOLETE Chemical transformation involving an ion." [PSI:MS] -comment: This child of the former purgatory term ion was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000438 -name: superelastic collision -def: "OBSOLETE Collision in which the translational energy of the fast-moving collision partner is increased at the expense of internal energy of one or both collision partners." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000439 -name: surface-induced reaction -def: "OBSOLETE A process wherein a reactant ion interacts with a surface to produce either chemically different species or a change in the internal energy of the reactant ion." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000440 -name: unimolecular dissociation -def: "OBSOLETE Fragmentation reaction in which the molecularity is treated as one, irrespective of whether the dissociative state is that of a metastable ion produced in the ion source or results from collisional excitation of a stable ion." [PSI:MS] -comment: This child of the former purgatory term ion reaction was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000441 -name: scan -def: "Function or process of the mass spectrometer where it records a spectrum." [PSI:MS] -relationship: part_of MS:1001458 ! spectrum generation information - -[Term] -id: MS:1000442 -name: spectrum -def: "Representation of intensity values corresponding to a range of measurement space." [PSI:MS] -relationship: part_of MS:1001458 ! spectrum generation information - -[Term] -id: MS:1000443 -name: mass analyzer type -def: "Mass analyzer separates the ions according to their mass-to-charge ratio." [PSI:MS] -relationship: part_of MS:1000451 ! mass analyzer - -[Term] -id: MS:1000444 -name: m/z Separation Method -def: "OBSOLETE Mass/charge separation Method." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000445 -name: sequential m/z separation method -def: "OBSOLETE Sequential m/z separation method." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000446 -name: fast ion bombardment -def: "The ionization of any species by the interaction of a focused beam of ions having a translational energy of several thousand eV with a solid sample." [PSI:MS] -synonym: "FIB" EXACT [] -is_a: MS:1000008 ! ionization type - -[Term] -id: MS:1000447 -name: LTQ -def: "Finnigan LTQ MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000448 -name: LTQ FT -def: "Finnigan LTQ FT MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000449 -name: LTQ Orbitrap -def: "Finnigan LTQ Orbitrap MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000450 -name: LXQ -def: "Finnigan LXQ MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000451 -name: mass analyzer -def: "Terms used to describe the Analyzer." [PSI:MS] -synonym: "analyzer" EXACT [] -relationship: part_of MS:1000463 ! instrument - -[Term] -id: MS:1000452 -name: data transformation -def: "Terms used to describe types of data processing." [PSI:MS] -synonym: "data processing" EXACT [] -relationship: part_of MS:1001458 ! spectrum generation information - -[Term] -id: MS:1000453 -name: detector -def: "The device that detects ions." [PSI:MS] -relationship: part_of MS:1000463 ! instrument - -[Term] -id: MS:1000454 -name: instrument additional description -def: "OBSOLETE Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000455 -name: ion selection attribute -def: "Ion selection properties that are associated with a value." [PSI:MS] -is_a: MS:1000547 ! object attribute -relationship: part_of MS:1000442 ! spectrum - -[Term] -id: MS:1000456 -name: precursor activation -def: "Terms to describe the precursor activation." [PSI:MS] -synonym: "activation" EXACT [] -relationship: part_of MS:1000442 ! spectrum - -[Term] -id: MS:1000457 -name: sample -def: "Terms to describe the sample." [PSI:MS] -relationship: part_of MS:1001458 ! spectrum generation information - -[Term] -id: MS:1000458 -name: source -def: "Terms to describe the source." [PSI:MS] -relationship: part_of MS:1000463 ! instrument - -[Term] -id: MS:1000459 -name: spectrum instrument description -def: "OBSOLETE Terms used to describe the spectrum." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000460 -name: unit -def: "OBSOLETE Terms to describe units." [PSI:MS] -comment: This term was made obsolete because it was redundant with the Unit Ontology term unit (UO:0000000). -relationship: part_of MS:1001458 ! spectrum generation information -is_obsolete: true - -[Term] -id: MS:1000461 -name: additional description -def: "OBSOLETE Terms to describe Additional." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000462 -name: ion optics -def: "Device used in the construction of a mass spectrometer to focus, contain or otherwise manipulate ions." [PSI:MS] -relationship: part_of MS:1000463 ! instrument - -[Term] -id: MS:1000463 -name: instrument -def: "Description of the instrument or the mass spectrometer." [PSI:MS] -synonym: "instrument configuration" EXACT [] -relationship: part_of MS:1001458 ! spectrum generation information - -[Term] -id: MS:1000464 -name: mass unit -def: "OBSOLETE A unit of measurement for mass." [PSI:MS] -comment: This term was made obsolete because it was redundant with Unit Ontology mass unit (UO:0000002). -is_obsolete: true - -[Term] -id: MS:1000465 -name: scan polarity -def: "Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer." [PSI:MS] -relationship: part_of MS:1000441 ! scan - -[Term] -id: MS:1000466 -name: alternating -def: "OBSOLETE Alternating." [PSI:MS] -comment: This term was made obsolete because . -is_obsolete: true - -[Term] -id: MS:1000467 -name: 1200 series LC/MSD SL -def: "The 1200 Series LC/MSD SL ion trap belongs to the Agilent LC/MSD ion trap family. It provides fast polarity switching and multisignal data acquisition capabilities in a single run while also providing 5 stages of automated data dependent MS2 and 11 stages of manual MS2." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1000468 -name: 6110 Quadrupole LC/MS -def: "The 6110 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with an entry level single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6110 Quadrupole mass spectrometer has m/z range of 10-1500 and 2500 u/s scan speed. It proves useful for wide range of SIM quantitative applications." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1000469 -name: 6120A Quadrupole LC/MS -def: "The 6120A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1000470 -name: 6130 Quadrupole LC/MS -def: "The 6130 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 series of Agilent mass spectrometers. The 6130 quadrupole mass spectrometer has m/z range of 2-3000, 2500 u/s scan speed in standard mode and 5250 u/s speed in fast-scan mode. It also uses multiple signal acquisition." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1000471 -name: 6140 Quadrupole LC/MS -def: "The 6140 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6140 Quadrupole mass spectrometer has m/z range of 10-1350, 2500 u/s scan speed in standard mode and 10000 u/s speed in fast-scan mode. It also uses multiple signal acquisition." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1000472 -name: 6210 Time-of-Flight LC/MS -def: "The 6210 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1000473 -name: 6310 Ion Trap LC/MS -def: "The 6310 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.35 resolution and mass range of 200-4000 with resolution of 3-4. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1000474 -name: 6320 Ion Trap LC/MS -def: "The 6320 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1000475 -name: 6330 Ion Trap LC/MS -def: "The 6330 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1000476 -name: 6340 Ion Trap LC/MS -def: "The 6340 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1000477 -name: 6410 Triple Quadrupole LC/MS -def: "The 6410 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. Mass range of the mass spectrometer is 15-1650 m/z, resolution is at three settings of 0.7 u (unit), 1.2 u (wide) and 2.5 u (widest). The mass accuracy for 6410 mass spectrometer is 0.1 across the mass range. The collision cell is a hexapole with linear acceleration." [PSI:MS] -synonym: "6410 Triple Quad LC/MS" EXACT [] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1000478 -name: 1200 series LC/MSD VL -def: "The LC/MSD VL ion trap is part of the family of Agilent ion trap mass spectrometers. It has ESI, APCI and APPI ion sources and is a useful ion trap when the amount of sample is not the limiting factor." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1000479 -name: purgatory -def: "OBSOLETE Terms that will likely become obsolete unless there are wails of dissent." [PSI:MS] -comment: The whole branch purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000480 -name: mass analyzer attribute -def: "Analyzer properties that are associated with a value." [PSI:MS] -relationship: part_of MS:1000451 ! mass analyzer - -[Term] -id: MS:1000481 -name: detector attribute -def: "Detector attribute recognized as a value." [PSI:MS] -relationship: part_of MS:1000453 ! detector - -[Term] -id: MS:1000482 -name: source attribute -def: "Property of a source device that need a value." [PSI:MS] -relationship: part_of MS:1000458 ! source - -[Term] -id: MS:1000483 -name: Thermo Fisher Scientific instrument model -def: "Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific." [PSI:MS] -synonym: "Thermo Scientific" RELATED [] -is_a: MS:1000031 ! instrument model - -[Term] -id: MS:1000484 -name: orbitrap -def: "An ion trapping device that consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution. The frequency of harmonic oscillations of the orbitally trapped ions along the axis of the electrostatic field is independent of the ion velocity and is inversely proportional to the square root of m/z so that the trap can be used as a mass analyzer." [PSI:MS] -is_a: MS:1000443 ! mass analyzer type - -[Term] -id: MS:1000485 -name: nanospray inlet -def: "Nanospray Inlet." [PSI:MS] -is_a: MS:1000057 ! electrospray inlet - -[Term] -id: MS:1000486 -name: source potential -def: "Potential difference at the MS source in volts." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000482 ! source attribute -relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000487 -name: ion optics attribute -def: "Ion optics involves components that help focus ion streams in mass spectrometry." [PSI:MS] -is_a: MS:1000462 ! ion optics - -[Term] -id: MS:1000488 -name: Hitachi instrument model -def: "Hitachi instrument model." [PSI:MS] -is_a: MS:1000031 ! instrument model - -[Term] -id: MS:1000489 -name: Varian instrument model -def: "Varian instrument model." [PSI:MS] -is_a: MS:1000031 ! instrument model - -[Term] -id: MS:1000490 -name: Agilent instrument model -def: "Agilent instrument model." [PSI:MS] -is_a: MS:1000031 ! instrument model - -[Term] -id: MS:1000491 -name: Dionex instrument model -def: "Dionex instrument model." [PSI:MS] -is_a: MS:1000031 ! instrument model - -[Term] -id: MS:1000492 -name: Thermo Electron instrument model -def: "Thermo Electron Corporation instrument model." [PSI:MS] -is_a: MS:1000483 ! Thermo Fisher Scientific instrument model - -[Term] -id: MS:1000493 -name: Finnigan MAT instrument model -def: "Finnigan MAT instrument model." [PSI:MS] -is_a: MS:1000483 ! Thermo Fisher Scientific instrument model - -[Term] -id: MS:1000494 -name: Thermo Scientific instrument model -def: "Thermo Scientific instrument model." [PSI:MS] -is_a: MS:1000483 ! Thermo Fisher Scientific instrument model - -[Term] -id: MS:1000495 -name: Applied Biosystems instrument model -def: "Applied Biosystems instrument model." [PSI:MS] -synonym: "ABI" EXACT [] -is_a: MS:1000031 ! instrument model - -[Term] -id: MS:1000496 -name: instrument attribute -def: "Instrument properties that are associated with a value." [PSI:MS] -is_a: MS:1000547 ! object attribute -relationship: part_of MS:1000463 ! instrument - -[Term] -id: MS:1000497 -name: zoom scan -def: "Special scan mode where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate." [PSI:MS] -synonym: "enhanced resolution scan" EXACT [] -is_a: MS:1000503 ! scan attribute - -[Term] -id: MS:1000498 -name: full scan -def: "OBSOLETE Feature of the ion trap mass spectrometer where MS data is acquired over a mass range." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000499 -name: spectrum attribute -def: "Nonphysical characteristic attributed to a spectrum." [PSI:MS] -relationship: part_of MS:1000442 ! spectrum - -[Term] -id: MS:1000500 -name: scan window upper limit -def: "The lower m/z bound of a mass spectrometer scan window." [PSI:MS] -synonym: "mzRangeStop" RELATED [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000549 ! selection window attribute -relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000501 -name: scan window lower limit -def: "The upper m/z bound of a mass spectrometer scan window." [PSI:MS] -synonym: "mzRangeStart" RELATED [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000549 ! selection window attribute -relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000502 -name: dwell time -def: "The time spent gathering data across a peak." [PSI:MS] -synonym: "Scan Duration" RELATED [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000503 ! scan attribute -relationship: has_units UO:0000010 ! second -relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000503 -name: scan attribute -def: "Nonphysical characteristic attributed to a spectrum acquisition scan." [PSI:MS] -is_a: MS:1000547 ! object attribute -relationship: part_of MS:1000441 ! scan - -[Term] -id: MS:1000504 -name: base peak m/z -def: "M/z value of the signal of highest intensity in the mass spectrum." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1003058 ! spectrum property -relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000505 -name: base peak intensity -def: "The intensity of the greatest peak in the mass spectrum." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1003058 ! spectrum property -relationship: has_units MS:1000131 ! number of detector counts -relationship: has_units MS:1000132 ! percent of base peak -relationship: has_units MS:1000814 ! counts per second -relationship: has_units MS:1000905 ! percent of base peak times 100 -relationship: has_units UO:0000269 ! absorbance unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000506 -name: ion role -def: "OBSOLETE Ion Role." [PSI:MS] -comment: This child of the former purgatory term ion was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000507 -name: ion property -def: "Nonphysical characteristic attributed to an ion." [PSI:MS] -relationship: part_of MS:1002806 ! ion - -[Term] -id: MS:1000508 -name: ion chemical type -def: "OBSOLETE Ion Type." [PSI:MS] -comment: This child of the former purgatory term ion was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000509 -name: activation energy -def: "Activation Energy." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000510 ! precursor activation attribute -relationship: has_units UO:0000266 ! electronvolt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000510 -name: precursor activation attribute -def: "Precursor Activation Attribute." [PSI:MS] -relationship: part_of MS:1000456 ! precursor activation - -[Term] -id: MS:1000511 -name: ms level -def: "Stage number achieved in a multi stage mass spectrometry acquisition." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1000499 ! spectrum attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1000512 -name: filter string -def: "A string unique to Thermo instrument describing instrument settings for the scan." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000503 ! scan attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000513 -name: binary data array -def: "A data array of values." [PSI:MS] -relationship: part_of MS:1000442 ! spectrum -relationship: part_of MS:1000625 ! chromatogram - -[Term] -id: MS:1000514 -name: m/z array -def: "A data array of m/z values." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000523 "64-bit float" -is_a: MS:1000513 ! binary data array -relationship: has_units MS:1000040 ! m/z - -[Term] -id: MS:1000515 -name: intensity array -def: "A data array of intensity values." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000523 "64-bit float" -is_a: MS:1000513 ! binary data array -relationship: has_units MS:1000131 ! number of detector counts -relationship: has_units MS:1000132 ! percent of base peak -relationship: has_units MS:1000814 ! counts per second -relationship: has_units MS:1000905 ! percent of base peak times 100 -relationship: has_units UO:0000269 ! absorbance unit - -[Term] -id: MS:1000516 -name: charge array -def: "A data array of charge values." [PSI:MS] -xref: binary-data-type:MS\:1000519 "32-bit integer" -is_a: MS:1000513 ! binary data array - -[Term] -id: MS:1000517 -name: signal to noise array -def: "A data array of signal-to-noise values." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000523 "64-bit float" -is_a: MS:1000513 ! binary data array - -[Term] -id: MS:1000518 -name: binary data type -def: "Encoding type of binary data specifying the binary representation and precision, e.g. 64-bit float." [PSI:MS] -relationship: part_of MS:1000442 ! spectrum -relationship: part_of MS:1000625 ! chromatogram - -[Term] -id: MS:1000519 -name: 32-bit integer -def: "Signed 32-bit little-endian integer." [PSI:MS] -is_a: MS:1000518 ! binary data type - -[Term] -id: MS:1000520 -name: 16-bit float -def: "OBSOLETE Signed 16-bit float." [PSI:MS] -is_a: MS:1000518 ! binary data type -is_obsolete: true - -[Term] -id: MS:1000521 -name: 32-bit float -def: "32-bit precision little-endian floating point conforming to IEEE-754." [PSI:MS] -is_a: MS:1000518 ! binary data type - -[Term] -id: MS:1000522 -name: 64-bit integer -def: "Signed 64-bit little-endian integer." [PSI:MS] -is_a: MS:1000518 ! binary data type - -[Term] -id: MS:1000523 -name: 64-bit float -def: "64-bit precision little-endian floating point conforming to IEEE-754." [PSI:MS] -is_a: MS:1000518 ! binary data type - -[Term] -id: MS:1000524 -name: data file content -def: "Describes the data content on the file." [PSI:MS] -relationship: part_of MS:1000577 ! source data file - -[Term] -id: MS:1000525 -name: spectrum representation -def: "Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks." [PSI:MS] -relationship: part_of MS:1000442 ! spectrum - -[Term] -id: MS:1000526 -name: Waters raw format -def: "Waters data file format found in a Waters RAW directory, generated from an MS acquisition." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1000527 -name: highest observed m/z -def: "Highest m/z value observed in the m/z array." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000808 ! chromatogram attribute -is_a: MS:1003058 ! spectrum property -relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000528 -name: lowest observed m/z -def: "Lowest m/z value observed in the m/z array." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000808 ! chromatogram attribute -is_a: MS:1003058 ! spectrum property -relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000529 -name: instrument serial number -def: "Serial Number of the instrument." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000496 ! instrument attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000530 -name: file format conversion -def: "Conversion of one file format to another." [PSI:MS] -is_a: MS:1000452 ! data transformation - -[Term] -id: MS:1000531 -name: software -def: "Software related to the recording or transformation of spectra." [PSI:MS] -relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies - -[Term] -id: MS:1000532 -name: Xcalibur -def: "Thermo Finnigan software for data acquisition and analysis." [PSI:MS] -is_a: MS:1000693 ! Thermo Finnigan software -is_a: MS:1001455 ! acquisition software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000533 -name: Bioworks -def: "Thermo Finnigan software for data analysis of peptides and proteins." [PSI:MS] -synonym: "Bioworks Browser" RELATED [] -is_a: MS:1000693 ! Thermo Finnigan software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000534 -name: MassLynx -def: "Micromass software for data acquisition and analysis." [PSI:MS] -is_a: MS:1000694 ! Waters software -is_a: MS:1001455 ! acquisition software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000535 -name: FlexAnalysis -def: "Bruker software for data analysis." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000536 -name: Data Explorer -def: "Applied Biosystems software for data acquisition and analysis." [PSI:MS] -is_a: MS:1000691 ! Applied Biosystems software -is_a: MS:1001455 ! acquisition software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000537 -name: 4700 Explorer -def: "Applied Biosystems software for data acquisition and analysis." [PSI:MS] -is_a: MS:1000691 ! Applied Biosystems software -is_a: MS:1001455 ! acquisition software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000538 -name: massWolf -def: "A software for converting Waters raw directory format to mzXML or mzML. MassWolf was originally developed at the Institute for Systems Biology." [PSI:MS] -synonym: "wolf" EXACT [] -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000539 -name: Voyager Biospectrometry Workstation System -def: "Applied Biosystems MALDI-TOF data acquisition and analysis system." [PSI:MS] -is_a: MS:1000691 ! Applied Biosystems software -is_a: MS:1001455 ! acquisition software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000540 -name: FlexControl -def: "Bruker software for data acquisition." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001455 ! acquisition software - -[Term] -id: MS:1000541 -name: ReAdW -def: "A software program for converting Thermo Finnigan RAW file format to mzXML or mzML. ReAdW was originally developed at the Institute for Systems Biology. Its whimsical interleaved spelling and capitalization is pronounced \"readraw\"." [PSI:MS] -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000542 -name: MzStar -def: "A software program for converting Applied Biosystems wiff file format to mzXML format. MzStar was originally developed at the Institute for Systems Biology. It is now obsoleted by the MzWiff program." [PSI:MS] -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000543 -name: data processing action -def: "Data processing attribute used to describe the type of data processing performed on the data file." [PSI:MS] -is_a: MS:1000452 ! data transformation - -[Term] -id: MS:1000544 -name: Conversion to mzML -def: "Conversion of a file format to Proteomics Standards Initiative mzML file format." [PSI:MS] -is_a: MS:1000530 ! file format conversion - -[Term] -id: MS:1000545 -name: Conversion to mzXML -def: "Conversion of a file format to Institute of Systems Biology mzXML file format." [PSI:MS] -is_a: MS:1000530 ! file format conversion - -[Term] -id: MS:1000546 -name: Conversion to mzData -def: "Conversion of a file format to Proteomics Standards Initiative mzData file format." [PSI:MS] -is_a: MS:1000530 ! file format conversion - -[Term] -id: MS:1000547 -name: object attribute -def: "Object Attribute." [PSI:MS] -relationship: part_of MS:1001458 ! spectrum generation information - -[Term] -id: MS:1000548 -name: sample attribute -def: "Sample properties that are associated with a value." [PSI:MS] -is_a: MS:1000547 ! object attribute -relationship: part_of MS:1000457 ! sample - -[Term] -id: MS:1000549 -name: selection window attribute -def: "Selection window properties that are associated with a value." [PSI:MS] -is_a: MS:1000547 ! object attribute -relationship: part_of MS:1000441 ! scan - -[Term] -id: MS:1000550 -name: time unit -def: "OBSOLETE Time Unit." [PSI:MS] -comment: This term was made obsolete because it was redundant with the Unit Ontology term time unit (UO:0000003). -is_obsolete: true - -[Term] -id: MS:1000551 -name: Analyst -def: "SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition." [PSI:MS] -is_a: MS:1000690 ! SCIEX software -is_a: MS:1001455 ! acquisition software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000552 -name: maldi spot identifier -def: "OBSOLETE Maldi Spot Identifier." [PSI:MS] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1000553 -name: Trapper -def: "A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology." [PSI:MS] -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000554 -name: LCQ Deca -def: "ThermoFinnigan LCQ Deca." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000555 -name: LTQ Orbitrap Discovery -def: "LTQ Orbitrap Discovery." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000556 -name: LTQ Orbitrap XL -def: "LTQ Orbitrap XL." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000557 -name: LTQ FT Ultra -def: "LTQ FT Ultra." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000558 -name: GC Quantum -def: "GC Quantum." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000559 -name: spectrum type -def: "Spectrum type." [PSI:MS] -relationship: part_of MS:1000442 ! spectrum - -[Term] -id: MS:1000560 -name: mass spectrometer file format -def: "The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format." [PSI:MS] -is_a: MS:1001459 ! file format - -[Term] -id: MS:1000561 -name: data file checksum type -def: "Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data." [PSI:MS] -relationship: part_of MS:1000577 ! source data file - -[Term] -id: MS:1000562 -name: ABI WIFF format -def: "Applied Biosystems WIFF file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1000563 -name: Thermo RAW format -def: "Thermo Scientific RAW file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1000564 -name: PSI mzData format -def: "Proteomics Standards Inititative mzData file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1000565 -name: Micromass PKL format -def: "Micromass PKL file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1000566 -name: ISB mzXML format -def: "Institute of Systems Biology mzXML file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1000567 -name: Bruker/Agilent YEP format -def: "Bruker/Agilent YEP file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1000568 -name: MD5 -def: "MD5 (Message-Digest algorithm 5) is a (now deprecated) cryptographic hash function with a 128-bit hash value used to check the integrity of files." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000561 ! data file checksum type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000569 -name: SHA-1 -def: "SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA). It is also used to verify file integrity. Since 2011 it has been deprecated by the NIST as a U. S. government standard." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000561 ! data file checksum type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000570 -name: spectra combination -def: "Method used to combine the mass spectra." [PSI:MS] -relationship: part_of MS:1000442 ! spectrum - -[Term] -id: MS:1000571 -name: sum of spectra -def: "Spectra Sum." [PSI:MS] -is_a: MS:1000570 ! spectra combination - -[Term] -id: MS:1000572 -name: binary data compression type -def: "Compression Type." [PSI:MS] -relationship: part_of MS:1000442 ! spectrum -relationship: part_of MS:1000625 ! chromatogram - -[Term] -id: MS:1000573 -name: median of spectra -def: "Spectra is combined by calculating the median of the spectra." [PSI:MS] -is_a: MS:1000570 ! spectra combination - -[Term] -id: MS:1000574 -name: zlib compression -def: "Zlib." [PSI:MS] -is_a: MS:1000572 ! binary data compression type - -[Term] -id: MS:1000575 -name: mean of spectra -def: "Spectra is combined by calculating the mean of the spectra." [PSI:MS] -is_a: MS:1000570 ! spectra combination - -[Term] -id: MS:1000576 -name: no compression -def: "No Compression." [PSI:MS] -is_a: MS:1000572 ! binary data compression type - -[Term] -id: MS:1000577 -name: source data file -def: "Data file from which an entity is sourced." [PSI:MS] -synonym: "source file" EXACT [] -relationship: part_of MS:1001458 ! spectrum generation information -is_a: MS:1000499 ! spectrum attribute - -[Term] -id: MS:1000578 -name: LCQ Fleet -def: "LCQ Fleet." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000579 -name: MS1 spectrum -def: "Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment." [PSI:MS] -synonym: "full spectrum" EXACT [] -synonym: "Q1 spectrum" EXACT [] -synonym: "Q3 spectrum" EXACT [] -synonym: "Single-Stage Mass Spectrometry" EXACT [] -is_a: MS:1000294 ! mass spectrum - -[Term] -id: MS:1000580 -name: MSn spectrum -def: "MSn refers to multi-stage MS2 experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n=2. Use the term ms level (MS:1000511) for specifying n." [PSI:MS] -synonym: "multiple-stage mass spectrometry spectrum" EXACT [] -synonym: "nth generation product ion spectrum" EXACT [] -synonym: "product ion spectrum" EXACT [] -is_a: MS:1000294 ! mass spectrum - -[Term] -id: MS:1000581 -name: CRM spectrum -def: "Spectrum generated from MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS] -is_a: MS:1000294 ! mass spectrum - -[Term] -id: MS:1000582 -name: SIM spectrum -def: "Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring)." [PSI:MS] -synonym: "MIM spectrum" EXACT [] -synonym: "multiple ion monitoring spectrum" EXACT [] -synonym: "selected ion monitoring spectrum" EXACT [] -is_a: MS:1000294 ! mass spectrum - -[Term] -id: MS:1000583 -name: SRM spectrum -def: "Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space." [PSI:MS] -synonym: "MRM spectrum" EXACT [] -synonym: "multiple reaction monitoring spectrum" EXACT [] -synonym: "selected reaction monitoring spectrum" EXACT [] -is_a: MS:1000294 ! mass spectrum - -[Term] -id: MS:1000584 -name: mzML format -def: "Proteomics Standards Inititative mzML file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1000585 -name: contact attribute -def: "Details about a person or organization to contact in case of concern or discussion about the file." [PSI:MS] -is_a: MS:1000547 ! object attribute -relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies - -[Term] -id: MS:1000586 -name: contact name -def: "Name of the contact person or organization." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000587 -name: contact address -def: "Postal address of the contact person or organization." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000588 -name: contact URL -def: "Uniform Resource Locator related to the contact person or organization." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000589 -name: contact email -def: "Email address of the contact person or organization." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000590 -name: contact affiliation -def: "Home institution of the contact person." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000591 -name: MzWiff -def: "A software program for converting Applied Biosystems wiff file format to the mzXML or mzML format. MzWiff is currently maintained at the Institute for Systems Biology. It replaces the slower mzStar program." [PSI:MS] -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000592 -name: smoothing -def: "A process of reducing spikes of intensity in order to reduce noise while preserving real peak signal. Many algorithms can be applied for this process." [PSI:MS] -is_a: MS:1000543 ! data processing action - -[Term] -id: MS:1000593 -name: baseline reduction -def: "A process of removal of varying intensities generated due to variable energy absorption before further processing can take place. Baseline reduction facilitates meaningful comparision between intensities of m/z values." [PSI:MS] -is_a: MS:1000543 ! data processing action - -[Term] -id: MS:1000594 -name: low intensity data point removal -def: "The removal of very low intensity data points that are likely to be spurious noise rather than real signal." [PSI:MS] -synonym: "thresholding" EXACT [] -is_a: MS:1001486 ! data filtering - -[Term] -id: MS:1000595 -name: time array -def: "A data array of relative time offset values from a reference time." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000523 "64-bit float" -is_a: MS:1000513 ! binary data array -relationship: has_units UO:0000010 ! second -relationship: has_units UO:0000031 ! minute - -[Term] -id: MS:1000596 -name: measurement method -def: "An attribute of resolution when recording the detector response in absence of the analyte." [PSI:MS] -relationship: part_of MS:1001458 ! spectrum generation information - -[Term] -id: MS:1000597 -name: ion optics type -def: "The electrical potential used to impart kinetic energy to ions in a mass spectrometer." [PSI:MS] -is_a: MS:1000462 ! ion optics - -[Term] -id: MS:1000598 -name: electron transfer dissociation -def: "A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons to them." [PSI:MS] -synonym: "ETD" EXACT [] -is_a: MS:1000044 ! dissociation method - -[Term] -id: MS:1000599 -name: pulsed q dissociation -def: "A process that involves precursor ion activation at high Q, a time delay to allow the precursor to fragment, then a rapid pulse to low Q where all fragment ions are trapped. The product ions can then be scanned out of the ion trap and detected." [PSI:MS] -synonym: "PQD" EXACT [] -is_a: MS:1000044 ! dissociation method - -[Term] -id: MS:1000600 -name: Proteios -def: "Database application and analysis platform for proteomics." [PSI:MS, source:http://www.proteios.org] -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000601 -name: ProteinLynx Global Server -def: "Waters software for data analysis." [PSI:MS] -is_a: MS:1000694 ! Waters software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000602 -name: Shimadzu MALDI-TOF instrument model -def: "Shimadzu MALDI-TOF instrument model." [PSI:MS] -is_a: MS:1000124 ! Shimadzu instrument model - -[Term] -id: MS:1000603 -name: Shimadzu Scientific Instruments instrument model -def: "Shimadzu Scientific Instruments instrument model." [PSI:MS] -is_a: MS:1000124 ! Shimadzu instrument model - -[Term] -id: MS:1000604 -name: LCMS-IT-TOF -def: "Shimadzu Scientific Instruments LCMS-IT-TOF MS." [PSI:MS] -is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model - -[Term] -id: MS:1000605 -name: LCMS-2010EV -def: "Shimadzu Scientific Instruments LCMS-2010EV MS." [PSI:MS] -is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model - -[Term] -id: MS:1000606 -name: LCMS-2010A -def: "Shimadzu Scientific Instruments LCMS-2010A MS." [PSI:MS] -is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model - -[Term] -id: MS:1000607 -name: AXIMA CFR MALDI-TOF -def: "Shimadzu Biotech AXIMA CFR MALDI-TOF MS." [PSI:MS] -is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model - -[Term] -id: MS:1000608 -name: AXIMA-QIT -def: "Shimadzu Biotech AXIMA-QIT MS." [PSI:MS] -is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model - -[Term] -id: MS:1000609 -name: AXIMA-CFR plus -def: "Shimadzu Biotech AXIMA-CFR plus MS." [PSI:MS] -is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model - -[Term] -id: MS:1000610 -name: AXIMA Performance MALDI-TOF/TOF -def: "Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS." [PSI:MS] -is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model - -[Term] -id: MS:1000611 -name: AXIMA Confidence MALDI-TOF -def: "Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS." [PSI:MS] -is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model - -[Term] -id: MS:1000612 -name: AXIMA Assurance Linear MALDI-TOF -def: "Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS." [PSI:MS] -is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model - -[Term] -id: MS:1000613 -name: DTA format -def: "SEQUEST DTA file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1000614 -name: ProteinLynx Global Server mass spectrum XML format -def: "Peak list file format used by ProteinLynx Global Server." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1000615 -name: ProteoWizard software -def: "ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb." [PSI:MS] -synonym: "pwiz" EXACT [] -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000616 -name: preset scan configuration -def: "A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo \"scan event\", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000503 ! scan attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000617 -name: wavelength array -def: "A data array of electromagnetic radiation wavelength values." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000523 "64-bit float" -is_a: MS:1000513 ! binary data array -relationship: has_units UO:0000018 ! nanometer - -[Term] -id: MS:1000618 -name: highest observed wavelength -def: "Highest wavelength observed in an EMR spectrum." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1003058 ! spectrum property -is_a: MS:1000808 ! chromatogram attribute -relationship: has_units UO:0000018 ! nanometer -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000619 -name: lowest observed wavelength -def: "Lowest wavelength observed in an EMR spectrum." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1003058 ! spectrum property -is_a: MS:1000808 ! chromatogram attribute -relationship: has_units UO:0000018 ! nanometer -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000620 -name: PDA spectrum -def: "OBSOLETE Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum)." [PSI:MS] -comment: This term was made obsolete because it was replaced by absorption spectrum (MS:1000806). -is_a: MS:1000524 ! data file content -is_a: MS:1000559 ! spectrum type -is_obsolete: true - -[Term] -id: MS:1000621 -name: photodiode array detector -def: "An array detector used to record spectra in the ultraviolet and visible region of light." [PSI:MS] -synonym: "PDA" EXACT [] -is_a: MS:1000345 ! array detector - -[Term] -id: MS:1000622 -name: Surveyor PDA -def: "Surveyor PDA." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000623 -name: Accela PDA -def: "Accela PDA." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000624 -name: inductive detector -def: "Inductive detector." [PSI:MS] -synonym: "image current detector" EXACT [] -is_a: MS:1000026 ! detector type - -[Term] -id: MS:1000625 -name: chromatogram -def: "Representation of a chromatographic separation attribute measurement versus time." [PSI:MS] -relationship: part_of MS:1001458 ! spectrum generation information - -[Term] -id: MS:1000626 -name: chromatogram type -def: "Type of chromatogram measurement being represented." [PSI:MS] -relationship: part_of MS:1000625 ! chromatogram - -[Term] -id: MS:1000627 -name: selected ion current chromatogram -def: "Representation of an array of the measurements of a specific single ion current versus time." [PSI:MS] -synonym: "SIC chromatogram" EXACT [] -is_a: MS:1000810 ! ion current chromatogram - -[Term] -id: MS:1000628 -name: basepeak chromatogram -def: "Representation of an array of the most intense peaks versus time." [PSI:MS] -is_a: MS:1000810 ! ion current chromatogram - -[Term] -id: MS:1000629 -name: low intensity threshold -def: "Threshold below which some action is taken." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000630 ! data processing parameter -relationship: has_units MS:1000131 ! number of detector counts -relationship: has_units MS:1000132 ! percent of base peak -relationship: has_units MS:1000814 ! counts per second -relationship: has_units MS:1000905 ! percent of base peak times 100 -relationship: has_units UO:0000269 ! absorbance unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000630 -name: data processing parameter -def: "Data processing parameter used in the data processing performed on the data file." [PSI:MS] -relationship: part_of MS:1001458 ! spectrum generation information - -[Term] -id: MS:1000631 -name: high intensity threshold -def: "Threshold above which some action is taken." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000630 ! data processing parameter -relationship: has_units MS:1000131 ! number of detector counts -relationship: has_units MS:1000132 ! percent of base peak -relationship: has_units MS:1000814 ! counts per second -relationship: has_units MS:1000905 ! percent of base peak times 100 -relationship: has_units UO:0000269 ! absorbance unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000632 -name: Q-Tof Premier -def: "Waters oa-ToF based Q-Tof Premier." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1000633 -name: possible charge state -def: "A possible charge state of the ion in a situation where the charge of an ion is known to be one of several possible values rather than a completely unknown value or determined to be a specific charge with reasonable certainty." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1000455 ! ion selection attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1000634 -name: DSQ -def: "ThermoFinnigan DSQ GC-MS." [PSI:MS] -is_a: MS:1000125 ! Thermo Finnigan instrument model - -[Term] -id: MS:1000635 -name: ITQ 700 -def: "Thermo Scientific ITQ 700 GC-MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000636 -name: ITQ 900 -def: "Thermo Scientific ITQ 900 GC-MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000637 -name: ITQ 1100 -def: "Thermo Scientific ITQ 1100 GC-MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000638 -name: LTQ XL ETD -def: "Thermo Scientific LTQ XL MS with ETD." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000639 -name: LTQ Orbitrap XL ETD -def: "Thermo Scientific LTQ Orbitrap XL MS with ETD." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000640 -name: DFS -def: "Thermo Scientific DFS HR GC-MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000641 -name: DSQ II -def: "Thermo Scientific DSQ II GC-MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000642 -name: MALDI LTQ XL -def: "Thermo Scientific MALDI LTQ XL MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000643 -name: MALDI LTQ Orbitrap -def: "Thermo Scientific MALDI LTQ Orbitrap MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000644 -name: TSQ Quantum Access -def: "Thermo Scientific TSQ Quantum Access MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000645 -name: Element XR -def: "Thermo Scientific Element XR HR-ICP-MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000646 -name: Element 2 -def: "Thermo Scientific Element 2 HR-ICP-MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000647 -name: Element GD -def: "Thermo Scientific Element GD Glow Discharge MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000648 -name: GC IsoLink -def: "Thermo Scientific GC IsoLink Isotope Ratio MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000649 -name: Exactive -def: "Thermo Scientific Exactive MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000650 -name: Proteome Discoverer -def: "Thermo Scientific software for data analysis of peptides and proteins." [PSI:MS] -is_a: MS:1000693 ! Thermo Finnigan software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000651 -name: 3200 QTRAP -def: "SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000652 -name: 4800 Plus MALDI TOF/TOF -def: "SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000653 -name: API 3200 -def: "SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000654 -name: API 5000 -def: "SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000655 -name: QSTAR Elite -def: "SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000656 -name: QSTAR Pulsar -def: "Applied Biosystems|MDS SCIEX QSTAR Pulsar." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000657 -name: QSTAR XL -def: "Applied Biosystems|MDS SCIEX QSTAR XL." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000658 -name: 4800 Proteomics Analyzer -def: "Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer." [PSI:MS] -is_a: MS:1000495 ! Applied Biosystems instrument model - -[Term] -id: MS:1000659 -name: 4000 Series Explorer Software -def: "SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS] -is_a: MS:1000690 ! SCIEX software -is_a: MS:1001455 ! acquisition software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000661 -name: GPS Explorer -def: "SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS] -is_a: MS:1000690 ! SCIEX software -is_a: MS:1001455 ! acquisition software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000662 -name: LightSight Software -def: "SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification." [PSI:MS] -is_a: MS:1000690 ! SCIEX software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000663 -name: ProteinPilot Software -def: "SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant." [PSI:MS] -is_a: MS:1000690 ! SCIEX software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000664 -name: TissueView Software -def: "Applied Biosystems|MDS SCIEX software for tissue imaging." [PSI:MS] -is_a: MS:1000690 ! SCIEX software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000665 -name: MarkerView Software -def: "Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling." [PSI:MS] -is_a: MS:1000690 ! SCIEX software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000666 -name: MRMPilot Software -def: "Applied Biosystems|MDS SCIEX software for MRM assay development." [PSI:MS] -is_a: MS:1000690 ! SCIEX software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000667 -name: BioAnalyst -def: "Applied Biosystems|MDS SCIEX software for bio-related data exploration." [PSI:MS] -is_a: MS:1000690 ! SCIEX software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000668 -name: Pro ID -def: "Applied Biosystems|MDS SCIEX software for protein identification." [PSI:MS] -is_a: MS:1000690 ! SCIEX software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000669 -name: Pro ICAT -def: "Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT." [PSI:MS] -is_a: MS:1000690 ! SCIEX software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000670 -name: Pro Quant -def: "Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ." [PSI:MS] -is_a: MS:1000690 ! SCIEX software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000671 -name: Pro BLAST -def: "Applied Biosystems|MDS SCIEX software for MS-BLAST identification." [PSI:MS] -is_a: MS:1000690 ! SCIEX software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000672 -name: Cliquid -def: "SCIEX Cliquid software for data analysis and quantitation." [PSI:MS] -is_a: MS:1000690 ! SCIEX software - -[Term] -id: MS:1000673 -name: MIDAS Workflow Designer -def: "Applied Biosystems|MDS SCIEX software for MRM assay development." [PSI:MS] -is_a: MS:1000690 ! SCIEX software - -[Term] -id: MS:1000674 -name: MultiQuant -def: "Applied Biosystems|MDS SCIEX software for MRM-based quantitation." [PSI:MS] -is_a: MS:1000690 ! SCIEX software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000675 -name: 6220 Time-of-Flight LC/MS -def: "The 6220 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1000676 -name: 6510 Quadrupole Time-of-Flight LC/MS -def: "The 6510 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1000677 -name: 6520A Quadrupole Time-of-Flight LC/MS -def: "The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1000678 -name: MassHunter Data Acquisition -def: "Software for data acquisition of 6000 series instruments." [PSI:MS] -is_a: MS:1000689 ! Agilent software -is_a: MS:1001455 ! acquisition software - -[Term] -id: MS:1000679 -name: MassHunter Easy Access -def: "Software for open access data acquisition." [PSI:MS] -is_a: MS:1000689 ! Agilent software -is_a: MS:1001455 ! acquisition software - -[Term] -id: MS:1000680 -name: MassHunter Qualitative Analysis -def: "Software for data analysis of data from 6000 series instruments." [PSI:MS] -is_a: MS:1000689 ! Agilent software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000681 -name: MassHunter Quantitative Analysis -def: "Software for quantitation of Triple Quadrupole and Quadrupole Time-of-Flight data." [PSI:MS] -is_a: MS:1000689 ! Agilent software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000682 -name: MassHunter Metabolite ID -def: "Software for identification of metabolites." [PSI:MS] -is_a: MS:1000689 ! Agilent software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000683 -name: MassHunter BioConfirm -def: "Software for protein characterization." [PSI:MS] -is_a: MS:1000689 ! Agilent software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000684 -name: Genespring MS -def: "Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data." [PSI:MS] -is_a: MS:1000689 ! Agilent software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000685 -name: MassHunter Mass Profiler -def: "Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data." [PSI:MS] -is_a: MS:1000689 ! Agilent software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000686 -name: METLIN -def: "Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites." [PSI:MS] -is_a: MS:1000689 ! Agilent software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000687 -name: Spectrum Mill for MassHunter Workstation -def: "Software for protein identification and characterization of complex protein digest mixtures." [PSI:MS] -is_a: MS:1000689 ! Agilent software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000688 -name: 6300 Series Ion Trap Data Analysis Software -def: "Software for data analysis of 6300 series ion trap mass spectrometers." [PSI:MS] -is_a: MS:1000689 ! Agilent software -is_a: MS:1001455 ! acquisition software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000689 -name: Agilent software -def: "Agilent software for data acquisition and analysis." [PSI:MS] -is_a: MS:1000531 ! software - -[Term] -id: MS:1000690 -name: SCIEX software -def: "SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS] -is_a: MS:1000531 ! software - -[Term] -id: MS:1000691 -name: Applied Biosystems software -def: "Applied Biosystems|MDS SCIEX software for data acquisition and analysis." [PSI:MS] -is_a: MS:1000531 ! software - -[Term] -id: MS:1000692 -name: Bruker software -def: "Bruker software for data acquisition and analysis." [PSI:MS] -is_a: MS:1000531 ! software - -[Term] -id: MS:1000693 -name: Thermo Finnigan software -def: "Thermo Finnigan software for data acquisition and analysis." [PSI:MS] -synonym: "Bioworks Browser" RELATED [] -is_a: MS:1000531 ! software - -[Term] -id: MS:1000694 -name: Waters software -def: "Waters software for data acquisition and analysis." [PSI:MS] -is_a: MS:1000531 ! software - -[Term] -id: MS:1000695 -name: apex ultra -def: "Bruker Daltonics' apex ultra: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS] -is_a: MS:1001556 ! Bruker Daltonics apex series - -[Term] -id: MS:1000696 -name: autoflex III smartbeam -def: "Bruker Daltonics' autoflex III smartbeam: MALDI TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1000697 -name: Bruker Daltonics HCT Series -def: "Bruker Daltonics' HCT Series." [PSI:MS] -is_a: MS:1000122 ! Bruker Daltonics instrument model - -[Term] -id: MS:1000698 -name: HCTultra -def: "Bruker Daltonics' HCTultra: ESI TOF, Nanospray, APCI, APPI." [PSI:MS] -is_a: MS:1000697 ! Bruker Daltonics HCT Series - -[Term] -id: MS:1000699 -name: HCTultra PTM -def: "Bruker Daltonics' HCTultra PTM: ESI TOF, Nanospray, APCI, APPI, PTR." [PSI:MS] -is_a: MS:1000697 ! Bruker Daltonics HCT Series - -[Term] -id: MS:1000700 -name: HCTultra ETD II -def: "Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI, APPI, ETD." [PSI:MS] -is_a: MS:1000697 ! Bruker Daltonics HCT Series - -[Term] -id: MS:1000701 -name: microflex LT -def: "Bruker Daltonics' microflex LT: MALDI TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1000702 -name: micrOTOF -def: "Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI." [PSI:MS] -is_a: MS:1001536 ! Bruker Daltonics micrOTOF series - -[Term] -id: MS:1000703 -name: micrOTOF-Q -def: "Bruker Daltonics' micrOTOF-Q: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] -is_a: MS:1001536 ! Bruker Daltonics micrOTOF series - -[Term] -id: MS:1000704 -name: micrOTOF-Q II -def: "Bruker Daltonics' micrOTOF-Q II: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] -is_a: MS:1001536 ! Bruker Daltonics micrOTOF series - -[Term] -id: MS:1000705 -name: ultraflex III TOF/TOF -def: "Bruker Daltonics' ultraflex III TOF/TOF: MALDI TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1000706 -name: apexControl -def: "Bruker software for data acquisition." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001455 ! acquisition software - -[Term] -id: MS:1000707 -name: BioTools -def: "Bruker software for data analysis." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000708 -name: CLINPROT -def: "Bruker CLINPROT software." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000709 -name: CLINPROT micro -def: "Bruker CLINPROT micro software." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000710 -name: CLINPROT robot -def: "Bruker CLINPROT robot software." [PSI:MS] -is_a: MS:1000692 ! Bruker software - -[Term] -id: MS:1000711 -name: ClinProTools -def: "Bruker ClinProTools software." [PSI:MS] -is_a: MS:1000692 ! Bruker software - -[Term] -id: MS:1000712 -name: Compass -def: "Bruker Compass software." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000713 -name: Compass for HCT/esquire -def: "Bruker Compass for HCT/esquire software." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000714 -name: Compass for micrOTOF -def: "Bruker Compass for micrOTOF software." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000715 -name: Compass OpenAccess -def: "Bruker compass OpenAccess software." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000716 -name: Compass Security Pack -def: "Bruker compass Security Pack software." [PSI:MS] -is_a: MS:1000692 ! Bruker software - -[Term] -id: MS:1000717 -name: CompassXport -def: "Bruker stand-alone software for data conversion." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000718 -name: CompassXtract -def: "Bruker software library for data access." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000719 -name: DataAnalysis -def: "Bruker software for data analysis." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000720 -name: dpControl -def: "Bruker software for data acquisition." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001455 ! acquisition software - -[Term] -id: MS:1000721 -name: esquireControl -def: "Bruker software for data acquisition." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001455 ! acquisition software - -[Term] -id: MS:1000722 -name: flexImaging -def: "Bruker software for data analysis." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000723 -name: GENOLINK -def: "Bruker GENOLINK software." [PSI:MS] -is_a: MS:1000692 ! Bruker software - -[Term] -id: MS:1000724 -name: GenoTools -def: "Bruker GenoTools software." [PSI:MS] -is_a: MS:1000692 ! Bruker software - -[Term] -id: MS:1000725 -name: HCTcontrol -def: "Bruker software for data acquisition." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001455 ! acquisition software - -[Term] -id: MS:1000726 -name: micrOTOFcontrol -def: "Bruker software for data acquisition." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001455 ! acquisition software - -[Term] -id: MS:1000727 -name: PolyTools -def: "Bruker PolyTools software." [PSI:MS] -is_a: MS:1000692 ! Bruker software - -[Term] -id: MS:1000728 -name: ProfileAnalysis -def: "Bruker software for data analysis." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000729 -name: PROTEINEER -def: "Bruker PROTEINEER software." [PSI:PI] -is_a: MS:1000692 ! Bruker software - -[Term] -id: MS:1000730 -name: PROTEINEER dp -def: "Bruker PROTEINEER dp software." [PSI:PI] -is_a: MS:1000692 ! Bruker software - -[Term] -id: MS:1000731 -name: PROTEINEER fc -def: "Bruker PROTEINEER fc software." [PSI:PI] -is_a: MS:1000692 ! Bruker software - -[Term] -id: MS:1000732 -name: PROTEINEER spII -def: "Bruker PROTEINEER spII software." [PSI:PI] -is_a: MS:1000692 ! Bruker software - -[Term] -id: MS:1000733 -name: PROTEINEER-LC -def: "Bruker PROTEINEER-LC software." [PSI:PI] -is_a: MS:1000692 ! Bruker software - -[Term] -id: MS:1000734 -name: ProteinScape -def: "Bruker ProteinScape software." [PSI:PI] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1000735 -name: PureDisk -def: "BrukerPureDisk software." [PSI:MS] -is_a: MS:1000692 ! Bruker software - -[Term] -id: MS:1000736 -name: QuantAnalysis -def: "Bruker software for data analysis." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000737 -name: spControl -def: "Bruker software for data acquisition." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001455 ! acquisition software - -[Term] -id: MS:1000738 -name: TargetAnalysis -def: "Bruker TargetAnalysis software." [PSI:MS] -is_a: MS:1000692 ! Bruker software - -[Term] -id: MS:1000739 -name: WARP-LC -def: "Bruker WARP-LC software." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001139 ! quantitation software name - -[Term] -id: MS:1000740 -name: parameter file -def: "Parameter file used to configure the acquisition of raw data on the instrument." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1000741 -name: Conversion to dta -def: "Conversion to dta format." [PSI:MS] -is_a: MS:1000530 ! file format conversion - -[Term] -id: MS:1000742 -name: Bioworks SRF format -def: "Thermo Finnigan SRF file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1000743 -name: TSQ Quantum Ultra AM -def: "Thermo Scientific TSQ Quantum Ultra AM." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000744 -name: selected ion m/z -def: "Mass-to-charge ratio of an selected ion." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000455 ! ion selection attribute -relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000745 -name: retention time alignment -def: "The correction of the spectrum scan times, as used e.g. in label-free proteomics." [PSI:MS] -is_a: MS:1000543 ! data processing action - -[Term] -id: MS:1000746 -name: high intensity data point removal -def: "The removal of very high intensity data points." [PSI:MS] -is_a: MS:1001486 ! data filtering - -[Term] -id: MS:1000747 -name: completion time -def: "The time that a data processing action was finished." [PSI:MS] -xref: value-type:xsd\:dateTime "The allowed value-type for this CV term." -is_a: MS:1000630 ! data processing parameter -relationship: has_value_type xsd\:dateTime ! The allowed value-type for this CV term - -[Term] -id: MS:1000748 -name: SSQ 7000 -def: "ThermoFinnigan SSQ 7000 MS." [PSI:MS] -is_a: MS:1000493 ! Finnigan MAT instrument model - -[Term] -id: MS:1000749 -name: TSQ 7000 -def: "ThermoFinnigan TSQ 7000 MS." [PSI:MS] -is_a: MS:1000493 ! Finnigan MAT instrument model - -[Term] -id: MS:1000750 -name: TSQ -def: "ThermoFinnigan TSQ MS." [PSI:MS] -is_a: MS:1000493 ! Finnigan MAT instrument model - -[Term] -id: MS:1000751 -name: TSQ Quantum Ultra -def: "Thermo Scientific TSQ Quantum Ultra." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000752 -name: TOPP software -def: "TOPP (The OpenMS proteomics pipeline) software." [PSI:MS] -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1000753 -name: BaselineFilter -def: "Removes the baseline from profile spectra using a top-hat filter." [PSI:MS] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1000754 -name: DBExporter -def: "Exports data from an OpenMS database to a file." [PSI:MS] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1000755 -name: DBImporter -def: "Imports data to an OpenMS database." [PSI:MS] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1000756 -name: FileConverter -def: "Converts between different MS file formats." [PSI:MS] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1000757 -name: FileFilter -def: "Extracts or manipulates portions of data from peak, feature or consensus feature files." [PSI:MS] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1000758 -name: FileMerger -def: "Merges several MS files into one file." [PSI:MS] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1000759 -name: InternalCalibration -def: "Applies an internal calibration." [PSI:MS] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1000760 -name: MapAligner -def: "OBSOLETE Corrects retention time distortions between maps." [PSI:MS] -comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP map aligner' (MS:1002147) branch. -is_a: MS:1000752 ! TOPP software -is_obsolete: true - -[Term] -id: MS:1000761 -name: MapNormalizer -def: "Normalizes peak intensities in an MS run." [PSI:MS] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1000762 -name: NoiseFilter -def: "OBSOLETE Removes noise from profile spectra by using different smoothing techniques." [PSI:MS] -comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP noise filter' (MS:1002131) branch. -is_a: MS:1000752 ! TOPP software -is_obsolete: true - -[Term] -id: MS:1000763 -name: PeakPicker -def: "OBSOLETE Finds mass spectrometric peaks in profile mass spectra." [PSI:MS] -comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP peak picker' (MS:1002134) branch. -is_a: MS:1000752 ! TOPP software -is_obsolete: true - -[Term] -id: MS:1000764 -name: Resampler -def: "Transforms an LC/MS map into a resampled map or a png image." [PSI:MS] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1000765 -name: SpectraFilter -def: "OBSOLETE Applies a filter to peak spectra." [PSI:MS] -comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP spectra filter' (MS:1002137) branch. -is_a: MS:1000752 ! TOPP software -is_obsolete: true - -[Term] -id: MS:1000766 -name: TOFCalibration -def: "Applies time of flight calibration." [PSI:MS] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1000767 -name: native spectrum identifier format -def: "Describes how the native spectrum identifiers are formated." [PSI:MS] -synonym: "nativeID format" EXACT [] -relationship: part_of MS:1000577 ! source data file - -[Term] -id: MS:1000768 -name: Thermo nativeID format -def: "Native format defined by controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger." [PSI:MS] -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1000769 -name: Waters nativeID format -def: "Native format defined by function=xsd:positiveInteger process=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS] -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1000770 -name: WIFF nativeID format -def: "Native format defined by sample=xsd:nonNegativeInteger period=xsd:nonNegativeInteger cycle=xsd:nonNegativeInteger experiment=xsd:nonNegativeInteger." [PSI:MS] -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1000771 -name: Bruker/Agilent YEP nativeID format -def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:MS] -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1000772 -name: Bruker BAF nativeID format -def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:MS] -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1000773 -name: Bruker FID nativeID format -def: "Native format defined by file=xsd:IDREF." [PSI:MS] -comment: The nativeID must be the same as the source file ID. -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1000774 -name: multiple peak list nativeID format -def: "Native format defined by index=xsd:nonNegativeInteger." [PSI:MS] -comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0. -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1000775 -name: single peak list nativeID format -def: "Native format defined by file=xsd:IDREF." [PSI:MS] -comment: The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different. -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1000776 -name: scan number only nativeID format -def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:MS] -comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived. -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1000777 -name: spectrum identifier nativeID format -def: "Native format defined by spectrum=xsd:nonNegativeInteger." [PSI:MS] -comment: Used for conversion from mzData. The spectrum id attribute is referenced. -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1000778 -name: charge state calculation -def: "A process that infers the charge state of an MSn spectrum's precursor(s) by the application of some algorithm." [PSI:MS] -is_a: MS:1000543 ! data processing action - -[Term] -id: MS:1000779 -name: below precursor intensity dominance charge state calculation -def: "Infers charge state as single or ambiguously multiple by determining the fraction of intensity below the precursor m/z." [PSI:MS] -is_a: MS:1000778 ! charge state calculation - -[Term] -id: MS:1000780 -name: precursor recalculation -def: "A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions." [PSI:MS] -is_a: MS:1000543 ! data processing action - -[Term] -id: MS:1000781 -name: msPrefix precursor recalculation -def: "Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans." [PSI:MS] -is_a: MS:1000780 ! precursor recalculation - -[Term] -id: MS:1000782 -name: Savitzky-Golay smoothing -def: "Reduces intensity spikes by applying local polynomial regression (of degree k) on a distribution (of at least k+1 equally spaced points) to determine the smoothed value for each point. It tends to preserve features of the distribution such as relative maxima, minima and width, which are usually 'flattened' by other adjacent averaging techniques." [PSI:MS] -is_a: MS:1000592 ! smoothing - -[Term] -id: MS:1000783 -name: LOWESS smoothing -def: "Reduces intensity spikes by applying a modelling method known as locally weighted polynomial regression. At each point in the data set a low-degree polynomial is fit to a subset of the data, with explanatory variable values near the point whose response is being estimated. The polynomial is fit using weighted least squares, giving more weight to points near the point whose response is being estimated and less weight to points further away. The value of the regression function for the point is then obtained by evaluating the local polynomial using the explanatory variable values for that data point. The LOESS fit is complete after regression function values have been computed for each of the n data points. Many of the details of this method, such as the degree of the polynomial model and the weights, are flexible." [PSI:MS] -is_a: MS:1000592 ! smoothing - -[Term] -id: MS:1000784 -name: Gaussian smoothing -def: "Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function." [PSI:MS] -synonym: "binomial smoothing" EXACT [] -synonym: "Weierstrass transform" EXACT [] -is_a: MS:1000592 ! smoothing - -[Term] -id: MS:1000785 -name: moving average smoothing -def: "Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect." [PSI:MS] -synonym: "box smoothing" EXACT [] -synonym: "boxcar smoothing" EXACT [] -synonym: "sliding average smoothing" EXACT [] -is_a: MS:1000592 ! smoothing - -[Term] -id: MS:1000786 -name: non-standard data array -def: "A data array that contains data not covered by any other term in this group. Please do not use this term, if the binary data array type might be commonly used - contact the PSI-MS working group in order to have another CV term added." [PSI:MS] -xref: binary-data-type:MS\:1000519 "32-bit integer" -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000522 "64-bit integer" -xref: binary-data-type:MS\:1000523 "64-bit float" -xref: binary-data-type:MS\:1001479 "null-terminated ASCII string" -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000513 ! binary data array -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000787 -name: inclusive low intensity threshold -def: "Threshold at or below which some action is taken." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000630 ! data processing parameter -relationship: has_units MS:1000131 ! number of detector counts -relationship: has_units MS:1000132 ! percent of base peak -relationship: has_units MS:1000814 ! counts per second -relationship: has_units MS:1000905 ! percent of base peak times 100 -relationship: has_units UO:0000269 ! absorbance unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000788 -name: inclusive high intensity threshold -def: "Threshold at or above which some action is taken." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000630 ! data processing parameter -relationship: has_units MS:1000131 ! number of detector counts -relationship: has_units MS:1000132 ! percent of base peak -relationship: has_units MS:1000814 ! counts per second -relationship: has_units MS:1000905 ! percent of base peak times 100 -relationship: has_units UO:0000269 ! absorbance unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000789 -name: enhanced multiply charged spectrum -def: "MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions." [PSI:MS] -is_a: MS:1000579 ! MS1 spectrum - -[Term] -id: MS:1000790 -name: time-delayed fragmentation spectrum -def: "MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation." [PSI:MS] -is_a: MS:1000580 ! MSn spectrum - -[Term] -id: MS:1000791 -name: enhanced resolution scan -def: "OBSOLETE Scan with enhanced resolution." [PSI:MS] -comment: This term was made obsolete because it was merged with zoom scan (MS:1000497). -is_obsolete: true - -[Term] -id: MS:1000792 -name: isolation window attribute -def: "Isolation window parameter." [PSI:MS] -is_a: MS:1000547 ! object attribute -relationship: part_of MS:1000441 ! scan - -[Term] -id: MS:1000793 -name: isolation window upper limit -def: "OBSOLETE The highest m/z being isolated in an isolation window." [PSI:MS] -comment: This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829. -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000792 ! isolation window attribute -relationship: has_units MS:1000040 ! m/z -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000794 -name: isolation window lower limit -def: "OBSOLETE The lowest m/z being isolated in an isolation window." [PSI:MS] -comment: This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829. -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000792 ! isolation window attribute -relationship: has_units MS:1000040 ! m/z -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000795 -name: no combination -def: "Use this term if only one scan was recorded or there is no information about scans available." [PSI:MS] -is_a: MS:1000570 ! spectra combination - -[Term] -id: MS:1000796 -name: spectrum title -def: "Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file." [PSI:MS] -comment: This is the preferred storage place for the spectrum TITLE from an MGF peak list. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001405 ! spectrum identification result details -is_a: MS:1000499 ! spectrum attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000797 -name: peak list scans -def: "A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS] -comment: This is the preferred storage place for the spectrum SCANS attribute from an MGF peak list. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001405 ! spectrum identification result details -is_a: MS:1003058 ! spectrum property -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000798 -name: peak list raw scans -def: "A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS] -comment: This is the preferred storage place for the spectrum RAWSCANS attribute from an MGF peak list. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001405 ! spectrum identification result details -is_a: MS:1003058 ! spectrum property -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000799 -name: custom unreleased software tool -def: "A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000531 ! software -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000800 -name: mass resolving power -def: "The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000503 ! scan attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000801 -name: area peak picking -def: "Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported." [PSI:MS] -synonym: "sum peak picking" EXACT [] -is_a: MS:1000035 ! peak picking - -[Term] -id: MS:1000802 -name: height peak picking -def: "Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported." [PSI:MS] -synonym: "max peak picking" EXACT [] -is_a: MS:1000035 ! peak picking - -[Term] -id: MS:1000803 -name: analyzer scan offset -def: "Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000503 ! scan attribute -relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000804 -name: electromagnetic radiation spectrum -def: "A plot of the relative intensity of electromagnetic radiation as a function of the wavelength." [PSI:MS] -synonym: "EMR spectrum" EXACT [] -is_a: MS:1000524 ! data file content -is_a: MS:1000559 ! spectrum type - -[Term] -id: MS:1000805 -name: emission spectrum -def: "A plot of the relative intensity of electromagnetic radiation emitted by atoms or molecules when excited." [PSI:MS] -is_a: MS:1000524 ! data file content -is_a: MS:1000559 ! spectrum type - -[Term] -id: MS:1000806 -name: absorption spectrum -def: "A plot of the relative intensity of electromagnetic radiation absorbed by atoms or molecules when excited." [PSI:MS] -is_a: MS:1000524 ! data file content -is_a: MS:1000559 ! spectrum type - -[Term] -id: MS:1000807 -name: Th/s -def: "Unit describing the scan rate of a spectrum in Thomson per second." [PSI:MS] -is_a: UO:0000000 ! unit - -[Term] -id: MS:1000808 -name: chromatogram attribute -def: "Chromatogram properties that are associated with a value." [PSI:MS] -is_a: MS:1000547 ! object attribute -relationship: part_of MS:1000625 ! chromatogram - -[Term] -id: MS:1000809 -name: chromatogram title -def: "A free-form text title describing a chromatogram." [PSI:MS] -comment: This is the preferred storage place for the spectrum title. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000808 ! chromatogram attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000810 -name: ion current chromatogram -def: "Representation of the current of ions versus time." [PSI:MS] -is_a: MS:1000524 ! data file content -is_a: MS:1000626 ! chromatogram type - -[Term] -id: MS:1000811 -name: electromagnetic radiation chromatogram -def: "Representation of electromagnetic properties versus time." [PSI:MS] -synonym: "EMR radiation chromatogram" EXACT [] -is_a: MS:1000524 ! data file content -is_a: MS:1000626 ! chromatogram type - -[Term] -id: MS:1000812 -name: absorption chromatogram -def: "Representation of light absorbed by the sample versus time." [PSI:MS] -is_a: MS:1000811 ! electromagnetic radiation chromatogram - -[Term] -id: MS:1000813 -name: emission chromatogram -def: "Representation of light emitted by the sample versus time." [PSI:MS] -is_a: MS:1000811 ! electromagnetic radiation chromatogram - -[Term] -id: MS:1000814 -name: counts per second -def: "The number of counted events observed per second in one or a group of elements of a detector." [PSI:MS] -is_a: MS:1000043 ! intensity unit - -[Term] -id: MS:1000815 -name: Bruker BAF format -def: "Bruker BAF raw file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1000816 -name: Bruker U2 format -def: "Bruker HyStar U2 file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1000817 -name: HyStar -def: "Bruker software for hyphenated experiments." [PSI:MS] -is_a: MS:1000692 ! Bruker software - -[Term] -id: MS:1000818 -name: Acquity UPLC PDA -def: "Acquity UPLC Photodiode Array Detector." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model -is_a: MS:1000621 ! photodiode array detector - -[Term] -id: MS:1000819 -name: Acquity UPLC FLR -def: "Acquity UPLC Fluorescence Detector." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model -is_a: MS:1002308 ! fluorescence detector - -[Term] -id: MS:1000820 -name: flow rate array -def: "A data array of flow rate measurements." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000523 "64-bit float" -is_a: MS:1000513 ! binary data array -relationship: has_units UO:0000271 ! microliters per minute - -[Term] -id: MS:1000821 -name: pressure array -def: "A data array of pressure measurements." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000523 "64-bit float" -is_a: MS:1000513 ! binary data array -relationship: has_units UO:0000110 ! pascal - -[Term] -id: MS:1000822 -name: temperature array -def: "A data array of temperature measurements." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000523 "64-bit float" -is_a: MS:1000513 ! binary data array -relationship: has_units UO:0000012 ! kelvin - -[Term] -id: MS:1000823 -name: Bruker U2 nativeID format -def: "Native format defined by declaration=xsd:nonNegativeInteger collection=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS] -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1000824 -name: no nativeID format -def: "No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format." [PSI:MS] -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1000825 -name: Bruker FID format -def: "Bruker FID file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1000826 -name: elution time -def: "The time of elution from all used chromatographic columns (one or more) in the chromatographic separation step, relative to the start of the chromatography." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000503 ! scan attribute -relationship: has_units UO:0000010 ! second -relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000827 -name: isolation window target m/z -def: "The primary or reference m/z about which the isolation window is defined." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000792 ! isolation window attribute -relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000828 -name: isolation window lower offset -def: "The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000792 ! isolation window attribute -relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000829 -name: isolation window upper offset -def: "The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000792 ! isolation window attribute -relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000831 -name: sample preparation -def: "Properties of the preparation steps which took place before the measurement was performed." [PSI:MS] -is_a: MS:1000547 ! object attribute -relationship: part_of MS:1000548 ! sample attribute - -[Term] -id: MS:1000832 -name: MALDI matrix application -def: "Attributes to describe the technique how the sample is prepared with the matrix solution." [PSI:MS] -relationship: part_of MS:1000831 ! sample preparation - -[Term] -id: MS:1000833 -name: matrix application type -def: "Describes the technique how the matrix is put on the sample target." [PSI:MS] -relationship: part_of MS:1000832 ! MALDI matrix application - -[Term] -id: MS:1000834 -name: matrix solution -def: "Describes the chemical solution used as matrix." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000832 ! MALDI matrix application -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000835 -name: matrix solution concentration -def: "Concentration of the chemical solution used as matrix." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000832 ! MALDI matrix application -relationship: has_units UO:0000175 ! gram per liter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000836 -name: dried droplet MALDI matrix preparation -def: "Dried droplet in MALDI matrix preparation." [PSI:MS] -is_a: MS:1000833 ! matrix application type - -[Term] -id: MS:1000837 -name: printed MALDI matrix preparation -def: "Printed MALDI matrix preparation." [PSI:MS] -is_a: MS:1000833 ! matrix application type - -[Term] -id: MS:1000838 -name: sprayed MALDI matrix preparation -def: "Sprayed MALDI matrix preparation." [PSI:MS] -is_a: MS:1000833 ! matrix application type - -[Term] -id: MS:1000839 -name: precoated MALDI sample plate -def: "Precoated MALDI sample plate." [PSI:MS] -is_a: MS:1000833 ! matrix application type -is_a: MS:1001938 ! sample plate type - -[Term] -id: MS:1000840 -name: laser -def: "Device that emits light (electromagnetic radiation) through a process called stimulated emission. The term is an acronym for Light Amplification by Stimulated Emission of Radiation." [PSI:MS] -relationship: part_of MS:1000482 ! source attribute - -[Term] -id: MS:1000841 -name: laser attribute -def: "Laser properties that are associated with a value." [PSI:MS] -relationship: part_of MS:1000840 ! laser - -[Term] -id: MS:1000842 -name: laser type -def: "Type of laser used for desorption purpose." [PSI:MS] -relationship: part_of MS:1000840 ! laser - -[Term] -id: MS:1000843 -name: wavelength -def: "OBSOLETE The distance between two peaks of the emitted laser beam." [PSI:MS] -comment: This term was made obsolete because it was redundant with the Pato Ontology term wavelength (UO:0001242). -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000841 ! laser attribute -relationship: has_units UO:0000018 ! nanometer -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000844 -name: focus diameter x -def: "Describes the diameter of the laser beam in x direction." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000841 ! laser attribute -relationship: has_units UO:0000017 ! micrometer -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000845 -name: focus diameter y -def: "Describes the diameter of the laser beam in y direction." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000841 ! laser attribute -relationship: has_units UO:0000017 ! micrometer -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000846 -name: pulse energy -def: "Describes output energy of the laser system. May be attenuated by filters or other means." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000841 ! laser attribute -relationship: has_units UO:0000112 ! joule -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000847 -name: pulse duration -def: "Describes how long the laser beam was emitted from the laser device." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000841 ! laser attribute -relationship: has_units UO:0000150 ! nanosecond -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000848 -name: attenuation -def: "Describes the reduction of the intensity of the laser beam energy." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000841 ! laser attribute -relationship: has_units UO:0000187 ! percent -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000849 -name: impact angle -def: "Describes the angle between the laser beam and the sample target." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000841 ! laser attribute -relationship: has_units UO:0000185 ! degree -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000850 -name: gas laser -def: "Laser which is powered by a gaseous medium." [PSI:MS] -is_a: MS:1000842 ! laser type - -[Term] -id: MS:1000851 -name: solid-state laser -def: "Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states." [PSI:MS] -is_a: MS:1000842 ! laser type - -[Term] -id: MS:1000852 -name: dye-laser -def: "Dye lasers use an organic dye as the gain medium." [PSI:MS] -is_a: MS:1000842 ! laser type - -[Term] -id: MS:1000853 -name: free electron laser -def: "Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term." [PSI:MS] -is_a: MS:1000842 ! laser type - -[Term] -id: MS:1000854 -name: LTQ XL -def: "Thermo Scientific LTQ XL MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000855 -name: LTQ Velos -def: "Thermo Scientific LTQ Velos MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000856 -name: LTQ Velos ETD -def: "Thermo Scientific LTQ Velos MS with ETD." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1000857 -name: run attribute -def: "Properties of the described run." [PSI:MS] -is_a: MS:1000547 ! object attribute - -[Term] -id: MS:1000858 -name: fraction identifier -def: "Identier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000857 ! run attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000859 -name: molecule -def: "Group of two or more atoms held together by chemical bonds." [https://en.wikipedia.org/wiki/Molecule] -is_a: MS:1000881 ! molecular entity - -[Term] -id: MS:1000860 -name: peptide -def: "A molecule of low molecular weight that is composed of two or more amino acid residues." [PSI:MS] -is_a: MS:1000859 ! molecule - -[Term] -id: MS:1000861 -name: molecular entity property -def: "A physical characteristic of a molecular entity." [PSI:MS] -relationship: part_of MS:1000881 ! molecular entity - -[Term] -id: MS:1000862 -name: isoelectric point -def: "The pH of a solution at which a charged molecule does not migrate in an electric field." [PSI:MS] -synonym: "pI" EXACT [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000861 ! molecular entity property -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000863 -name: predicted isoelectric point -def: "The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm." [PSI:MS] -synonym: "predicted pI" EXACT [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000862 ! isoelectric point -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000864 -name: chemical formula -def: "A combination of symbols used to express the chemical composition of a molecule." [EDAM:0846] -is_a: MS:1003033 ! molecular entity attribute - -[Term] -id: MS:1000865 -name: empirical formula -def: "A chemical formula which expresses the proportions of the elements present in a substance." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000864 ! chemical formula -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000866 -name: molecular formula -def: "A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000864 ! chemical formula -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000867 -name: structural formula -def: "A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000864 ! chemical formula -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000868 -name: SMILES formula -def: "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string." [EDAM:2301] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000864 ! chemical formula -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000869 -name: collision gas pressure -def: "The gas pressure of the collision gas used for collisional excitation." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000510 ! precursor activation attribute -relationship: has_units UO:0000110 ! pascal -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000870 -name: 4000 QTRAP -def: "OBSOLETE SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000." [PSI:MS] -comment: This term was obsoleted because was redundant to MS:1000139. -is_a: MS:1000121 ! SCIEX instrument model -is_obsolete: true - -[Term] -id: MS:1000871 -name: SRM software -def: "Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs." [PSI:MS] -is_a: MS:1000531 ! software - -[Term] -id: MS:1000872 -name: MaRiMba -def: "Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology." [http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba] -is_a: MS:1000871 ! SRM software - -[Term] -id: MS:1000873 -name: peptide attribute calculation software -def: "Software used to predict or calculate numerical attributes of peptides." [PSI:MS] -is_a: MS:1000531 ! software - -[Term] -id: MS:1000874 -name: SSRCalc -def: "Sequence Specific Retention Calculator estimates the retention time of peptides based on their sequence." [http://hs2.proteome.ca/SSRCalc/SSRCalc.html] -is_a: MS:1000873 ! peptide attribute calculation software - -[Term] -id: MS:1000875 -name: declustering potential -def: "Potential difference between the orifice and the skimmer in volts." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000482 ! source attribute -relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000876 -name: cone voltage -def: "Potential difference between the sampling cone/orifice in volts." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000482 ! source attribute -relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000877 -name: tube lens voltage -def: "Potential difference setting of the tube lens in volts." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000482 ! source attribute -relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000878 -name: external reference identifier -def: "An identifier/accession number to an external reference database." [PSI:MS] -is_a: MS:1002840 ! external reference data - -[Term] -id: MS:1000879 -name: PubMed identifier -def: "A unique identifier for a publication in the PubMed database (MIR:00000015)." [PSI:MS] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1000880 -name: interchannel delay -def: "The duration of intervals between scanning, during which the instrument configuration is switched." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000503 ! scan attribute -relationship: has_units UO:0000010 ! second -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000881 -name: molecular entity -def: "Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity." [https://en.wikipedia.org/wiki/Molecular_entity] -relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies - -[Term] -id: MS:1000882 -name: protein -def: "A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA of a gene." [PSI:MS] -is_a: MS:1000859 ! molecule - -[Term] -id: MS:1000883 -name: protein short name -def: "A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN)." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000884 ! protein attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000884 -name: protein attribute -def: "An nonphysical characterstic attributed to a specific protein." [PSI:MS] -relationship: part_of MS:1000882 ! protein -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1000885 -name: protein accession -def: "Identifier for a specific protein in a database." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000884 ! protein attribute -is_a: MS:1003046 ! peptide-to-protein mapping attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000886 -name: protein name -def: "A long name describing the function of the protein." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000884 ! protein attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000887 -name: peptide attribute -def: "Nonphysical characteristic attributed to a peptide." [PSI:MS] -relationship: part_of MS:1000860 ! peptide - -[Term] -id: MS:1000888 -name: stripped peptide sequence -def: "Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1003050 ! peptidoform attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000889 -name: peptidoform sequence -def: "Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present." [PSI:MS] -comment: Make it more general as there are actually many other ways to display a modified peptide sequence. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1003050 ! peptidoform attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000890 -name: peptidoform labeling state -def: "A state description of how a peptide might be isotopically or isobarically labelled." [PSI:MS] -is_a: MS:1003050 ! peptidoform attribute - -[Term] -id: MS:1000891 -name: heavy labeled peptidoform -def: "A peptide that has been created or labelled with some heavier-than-usual isotopes." [PSI:MS] -is_a: MS:1000890 ! peptidoform labeling state - -[Term] -id: MS:1000892 -name: unlabeled peptidoform -def: "A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as \"light\" to distinguish from \"heavy\"." [PSI:MS] -synonym: "light labeled peptide" EXACT [] -is_a: MS:1000890 ! peptidoform labeling state - -[Term] -id: MS:1000893 -name: peptidoform group label -def: "An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1003050 ! peptidoform attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000894 -name: retention time -def: "A time interval from the start of chromatography when an analyte exits a chromatographic column." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1003050 ! peptidoform attribute -relationship: has_units UO:0000010 ! second -relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000895 -name: local retention time -def: "A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000894 ! retention time -relationship: has_units UO:0000010 ! second -relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000896 -name: normalized retention time -def: "A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000894 ! retention time -relationship: has_units UO:0000010 ! second -relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000897 -name: predicted retention time -def: "A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000894 ! retention time -relationship: has_units UO:0000010 ! second -relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000898 -name: standard -def: "Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence." [PSI:MS] -relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies - -[Term] -id: MS:1000899 -name: de facto standard -def: "A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard." [PSI:MS] -is_a: MS:1000898 ! standard - -[Term] -id: MS:1000900 -name: minimum information standard -def: "A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result." [PSI:MS] -is_a: MS:1000898 ! standard - -[Term] -id: MS:1000901 -name: retention time normalization standard -def: "A standard providing the retention times at which a set of reference compounds exit the reference chromatographic column." [PSI:MS] -is_a: MS:1000898 ! standard - -[Term] -id: MS:1000902 -name: H-PINS retention time normalization standard -def: "The de facto standard providing the retention times at which a set of halogenated reference peptides exit the reference chromatographic column." [DOI:10.1074/mcp.M800569-MCP200, PMID:19411281] -is_a: MS:1000901 ! retention time normalization standard - -[Term] -id: MS:1000903 -name: product ion series ordinal -def: "The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion)." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1001221 ! product ion attribute -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1000904 -name: product ion m/z delta -def: "The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z." [PSI:PI] -is_a: MS:1001221 ! product ion attribute -relationship: has_units MS:1000040 ! m/z - -[Term] -id: MS:1000905 -name: percent of base peak times 100 -def: "The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000043 ! intensity unit -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000906 -name: peak intensity rank -def: "Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc." [PSI:MS] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1000455 ! ion selection attribute -relationship: part_of MS:1000231 ! peak -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1000907 -name: peak targeting suitability rank -def: "Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitability peak is 2, etc. Suitability is algorithm and context dependant." [PSI:MS] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1000455 ! ion selection attribute -relationship: part_of MS:1000231 ! peak -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1000908 -name: transition -def: "A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely." [PSI:MS] -synonym: "reaction" EXACT [] -relationship: part_of MS:1001458 ! spectrum generation information - -[Term] -id: MS:1000909 -name: transition validation method -def: "The strategy used to validate that a transition is effective." [PSI:MS] -relationship: part_of MS:1000908 ! transition - -[Term] -id: MS:1000910 -name: transition optimized on specified instrument -def: "The transition has been optimized by direct injection of the peptide into an instrument specified in a separate term, and the optimum voltages and fragmentation energies have been determined." [PSI:MS] -is_a: MS:1000909 ! transition validation method - -[Term] -id: MS:1000911 -name: transition validated with an MS/MS spectrum on specified instrument -def: "The transition has been validated by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term." [PSI:MS] -is_a: MS:1000909 ! transition validation method - -[Term] -id: MS:1000912 -name: transition purported from an MS/MS spectrum on a different, specified instrument -def: "The transition has been purported by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. However, the detecting instrument is of a different type (e.g. ion trap) than the instrument that the transition will eventually be used on (e.g. triple quad)." [PSI:MS] -is_a: MS:1000909 ! transition validation method - -[Term] -id: MS:1000913 -name: transition predicted by informatic analysis -def: "The transition has been predicted by informatics software without any direct spectral evidence." [PSI:MS] -is_a: MS:1000909 ! transition validation method - -[Term] -id: MS:1000914 -name: tab delimited text format -def: "A file format that has two or more columns of tabular data where each column is separated by a TAB character." [PSI:MS] -is_a: MS:1001459 ! file format -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1000915 -name: retention time window attribute -def: "An attribute of a window in time about which a peptide might elute from the column." [PSI:MS] -relationship: part_of MS:1000894 ! retention time - -[Term] -id: MS:1000916 -name: retention time window lower offset -def: "The extent of the retention time window in time units below the target retention time. The lower and upper offsets may be asymmetric about the target time." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000915 ! retention time window attribute -relationship: has_units UO:0000010 ! second -relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000917 -name: retention time window upper offset -def: "The extent of the retention time window in time units above the target retention time. The lower and upper offsets may be asymmetric about the target time." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000915 ! retention time window attribute -relationship: has_units UO:0000010 ! second -relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000918 -name: target list -def: "A list of peptides or compounds and their expected m/z coordinates that can be used to cause a mass spectrometry to obtain spectra of those molecules specifically." [PSI:MS] -relationship: part_of MS:1001458 ! spectrum generation information - -[Term] -id: MS:1000919 -name: target inclusion exclusion priority -def: "A priority setting specifying whether included or excluded targets have priority over the other." [PSI:MS] -relationship: part_of MS:1000918 ! target list - -[Term] -id: MS:1000920 -name: includes supersede excludes -def: "A priority setting specifying that included targets have priority over the excluded targets if there is a conflict." [PSI:MS] -is_a: MS:1000919 ! target inclusion exclusion priority - -[Term] -id: MS:1000921 -name: excludes supersede includes -def: "A priority setting specifying that excluded targets have priority over the included targets if there is a conflict." [PSI:MS] -is_a: MS:1000919 ! target inclusion exclusion priority - -[Term] -id: MS:1000922 -name: Skyline -def: "Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington." [https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default] -is_a: MS:1000871 ! SRM software -is_a: MS:1001139 ! quantitation software name - -[Term] -id: MS:1000923 -name: TIQAM -def: "Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology." [http://tools.proteomecenter.org/TIQAM/TIQAM.html] -is_a: MS:1000871 ! SRM software - -[Term] -id: MS:1000924 -name: MaRiMba -def: "OBSOLETE Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology." [http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba] -comment: This term was made obsolete because it was redundant with an existing term (MS:1000872). -is_obsolete: true -replaced_by: MS:1000872 - -[Term] -id: MS:1000925 -name: ATAQS -def: "Software suite used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the Institute for Systems Biology." [PSI:MS] -is_a: MS:1000871 ! SRM software - -[Term] -id: MS:1000926 -name: product interpretation rank -def: "The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1." [PSI:MS] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1001221 ! product ion attribute -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1000927 -name: ion injection time -def: "The length of time spent filling an ion trapping device." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000503 ! scan attribute -relationship: has_units UO:0000028 ! millisecond -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1000928 -name: calibration spectrum -def: "A spectrum derived from a special calibration source, rather than from the primary injected sample. A calibration spectrum is typically derived from a substance that can be used to correct systematic shift in m/z for spectra of the primary inject sample." [PSI:MS] -is_a: MS:1000559 ! spectrum type - -[Term] -id: MS:1000929 -name: Shimadzu Biotech nativeID format -def: "Native format defined by source=xsd:string start=xsd:nonNegativeInteger end=xsd:nonNegativeInteger." [PSI:MS] -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1000930 -name: Shimadzu Biotech database entity -def: "Shimadzu Biotech format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1000931 -name: QTRAP 5500 -def: "Applied Biosystems|MDS SCIEX QTRAP 5500." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000932 -name: TripleTOF 5600 -def: "SCIEX TripleTOF 5600, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1000933 -name: protein modifications -def: "Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000884 ! protein attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1000934 -name: gene name -def: "Name of the gene from which the protein is translated." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000884 ! protein attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001000 -name: spectrum interpretation -def: "Collection of terms from the PSI Proteome Informatics standards describing the interpretation of spectra." [PSI:PI] -relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies - -[Term] -id: MS:1001005 -name: SEQUEST:CleavesAt -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001006 -name: SEQUEST:ViewCV -def: "SEQUEST View Input Parameters." [PSI:PI] -is_a: MS:1002096 ! SEQUEST input parameter - -[Term] -id: MS:1001007 -name: SEQUEST:OutputLines -def: "Number of peptide results to show." [PSI:MS] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001009 -name: SEQUEST:DescriptionLines -def: "Number of full protein descriptions to show for top N peptides." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001010 -name: de novo search -def: "A de novo sequencing search (without database)." [PSI:PI] -is_a: MS:1001080 ! search type - -[Term] -id: MS:1001011 -name: search database details -def: "Details about the database searched." [PSI:PI] -is_a: MS:1001249 ! search input details - -[Term] -id: MS:1001012 -name: database source -def: "The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001013 -name: database name -def: "The name of the search database (nr, SwissProt or est_human)." [PSI:PI] -is_a: MS:1001011 ! search database details - -[Term] -id: MS:1001014 -name: database local file path -def: "OBSOLETE: Use attribute in mzIdentML instead. Local file path of the search database from the search engine's point of view." [PSI:PI] -is_a: MS:1001011 ! search database details -is_obsolete: true - -[Term] -id: MS:1001015 -name: database original uri -def: "URI, from where the search database was originally downloaded." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." -is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term - -[Term] -id: MS:1001016 -name: database version -def: "Version of the search database. In mzIdentML use the attribute instead." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001017 -name: database release date -def: "OBSOLETE: Use attribute in mzIdentML instead. Release date of the search database." [PSI:PI] -is_a: MS:1001011 ! search database details -is_obsolete: true - -[Term] -id: MS:1001018 -name: database type -def: "Database containing amino acid or nucleic acid sequences." [PSI:PI] -is_a: MS:1001011 ! search database details - -[Term] -id: MS:1001019 -name: database filtering -def: "Was there filtering used on the database." [PSI:PI] -is_a: MS:1001011 ! search database details - -[Term] -id: MS:1001020 -name: DB filter taxonomy -def: "A taxonomy filter was to the database search." [PSI:PI] -is_a: MS:1001511 ! Sequence database filter types - -[Term] -id: MS:1001021 -name: DB filter on accession numbers -def: "Filtering applied specifically by accession number pattern." [PSI:PI] -is_a: MS:1001511 ! Sequence database filter types - -[Term] -id: MS:1001022 -name: DB MW filter -def: "Filtering applied specifically by protein molecular weight, specified as either a range or above/below a threshold value." [PSI:PI] -is_a: MS:1001511 ! Sequence database filter types - -[Term] -id: MS:1001023 -name: DB PI filter -def: "Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value." [PSI:PI] -is_a: MS:1001511 ! Sequence database filter types - -[Term] -id: MS:1001024 -name: translation frame -def: "The translated open reading frames from a nucleotide database considered in the search (range: 1-6)." [PSI:PI] -is_a: MS:1001011 ! search database details - -[Term] -id: MS:1001025 -name: translation table -def: "The translation table used to translate the nucleotides to amino acids." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001026 -name: SEQUEST:NormalizeXCorrValues -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001027 -name: DB filter on sequence pattern -def: "Filtering applied specifically by amino acid sequence pattern." [PSI:PI] -is_a: MS:1001511 ! Sequence database filter types - -[Term] -id: MS:1001028 -name: SEQUEST:SequenceHeaderFilter -def: "String in the header of a sequence entry for that entry to be searched." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001029 -name: number of sequences searched -def: "The number of sequences (proteins / nucleotides) from the database search after filtering." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001030 -name: number of peptide seqs compared to each spectrum -def: "Number of peptide seqs compared to each spectrum." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1001011 ! search database details -is_a: MS:1001405 ! spectrum identification result details -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001031 -name: spectral library search -def: "A search using a library of spectra." [PSI:PI] -is_a: MS:1001080 ! search type - -[Term] -id: MS:1001032 -name: SEQUEST:SequencePartialFilter -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001035 -name: date / time search performed -def: "OBSOLETE: use attribute in mzIdentML instead. Date and time of the actual search run." [PSI:PI] -is_a: MS:1001184 ! search statistics -is_obsolete: true - -[Term] -id: MS:1001036 -name: search time taken -def: "The time taken to complete the search in seconds." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1001184 ! search statistics -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001037 -name: SEQUEST:ShowFragmentIons -def: "Flag indicating that fragment ions should be shown." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001038 -name: SEQUEST:Consensus -def: "Specify depth as value of the CVParam." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1001006 ! SEQUEST:ViewCV -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001040 -name: intermediate analysis format -def: "Type of the source file, the mzIdentML was created from." [PSI:PI] -is_a: MS:1001459 ! file format - -[Term] -id: MS:1001041 -name: SEQUEST:sortCV -def: "SEQUEST View / Sort Input Parameters." [PSI:PI] -is_a: MS:1001006 ! SEQUEST:ViewCV - -[Term] -id: MS:1001042 -name: SEQUEST:LimitTo -def: "Specify \"number of dtas shown\" as value of the CVParam." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1002096 ! SEQUEST input parameter -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001044 -name: cleavage agent details -def: "Details of cleavage agent (enzyme)." [PSI:PI] -is_a: MS:1001249 ! search input details - -[Term] -id: MS:1001045 -name: cleavage agent name -def: "The name of the cleavage agent." [PSI:PI] -is_a: MS:1001044 ! cleavage agent details - -[Term] -id: MS:1001046 -name: SEQUEST:sort by dCn -def: "Sort order of SEQUEST search results by the delta of the normalized correlation score." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001047 -name: SEQUEST:sort by dM -def: "Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001048 -name: SEQUEST:sort by Ions -def: "Sort order of SEQUEST search results given by the ions." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001049 -name: SEQUEST:sort by MH+ -def: "Sort order of SEQUEST search results given by the mass of the protonated ion." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001050 -name: SEQUEST:sort by P -def: "Sort order of SEQUEST search results given by the probability." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001051 -name: multiple enzyme combination rules -def: "OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001052 -name: SEQUEST:sort by PreviousAminoAcid -def: "Sort order of SEQUEST search results given by the previous amino acid." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001053 -name: SEQUEST:sort by Ref -def: "Sort order of SEQUEST search results given by the reference." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001055 -name: modification parameters -def: "Modification parameters for the search engine run." [PSI:PI] -relationship: part_of MS:1001000 ! spectrum interpretation - -[Term] -id: MS:1001056 -name: modification specificity rule -def: "The specificity rules for the modifications applied by the search engine." [PSI:PI] -is_a: MS:1001055 ! modification parameters - -[Term] -id: MS:1001057 -name: tolerance on types -def: "OBSOLETE: Tolerance on types." [PSI:PI] -is_a: MS:1001055 ! modification parameters -is_obsolete: true - -[Term] -id: MS:1001058 -name: quality estimation by manual validation -def: "The quality estimation was done manually." [PSI:PI] -is_a: MS:1001060 ! quality estimation method details - -[Term] -id: MS:1001059 -name: SEQUEST:sort by RSp -def: "Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide)." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001060 -name: quality estimation method details -def: "Method for quality estimation (manually or with decoy database)." [PSI:PI] -is_a: MS:1001249 ! search input details - -[Term] -id: MS:1001061 -name: neutral loss -def: "OBSOLETE: replaced by MS:1000336 (neutral loss): Leave this to PSI-MOD." [PSI:PI] -is_a: MS:1001055 ! modification parameters -is_obsolete: true -replaced_by: MS:1000336 - -[Term] -id: MS:1001062 -name: Mascot MGF format -def: "Mascot MGF file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1001065 -name: TODOscoring model -def: "OBSOLETE: There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms." [PSI:PI] -comment: This term was made obsolete and is replaced by the term (MS:1001961). -is_a: MS:1001249 ! search input details -is_obsolete: true -replaced_by: MS:1001961 - -[Term] -id: MS:1001066 -name: ions series considered in search -def: "The description of the DEPRECATED ion fragment series (including charges and neutral losses) that are considered by the search engine." [PSI:PI] -is_a: MS:1001249 ! search input details - -[Term] -id: MS:1001068 -name: SEQUEST:sort by Sp -def: "Sort order of SEQUEST search results by the Sp score." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001069 -name: SEQUEST:sort by TIC -def: "Sort order of SEQUEST search results given by the total ion current." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001070 -name: SEQUEST:sort by Scan -def: "Sort order of SEQUEST search results given by the scan number." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001071 -name: SEQUEST:sort by Sequence -def: "Sort order of SEQUEST search results given by the sequence." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001072 -name: SEQUEST:sort by Sf -def: "Sort order of SEQUEST search results given by the SEQUEST result 'Sf'." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001073 -name: database type amino acid -def: "Database contains amino acid sequences." [PSI:PI] -is_a: MS:1001018 ! database type - -[Term] -id: MS:1001079 -name: database type nucleotide -def: "Database contains nucleic acid sequences." [PSI:PI] -is_a: MS:1001018 ! database type - -[Term] -id: MS:1001080 -name: search type -def: "Enumeration of type of search value (i.e. from PMF, sequence tag, MS2)." [PSI:PI] -is_a: MS:1001249 ! search input details - -[Term] -id: MS:1001081 -name: pmf search -def: "A peptide mass fingerprint search." [PSI:PI] -is_a: MS:1001080 ! search type - -[Term] -id: MS:1001082 -name: tag search -def: "A sequence tag search." [PSI:PI] -is_a: MS:1001080 ! search type - -[Term] -id: MS:1001083 -name: ms-ms search -def: "An MS2 search (with fragment ions)." [PSI:PI] -is_a: MS:1001080 ! search type - -[Term] -id: MS:1001084 -name: database nr -def: "Non-redundant GenBank sequence database." [PSI:PI] -is_a: MS:1001013 ! database name - -[Term] -id: MS:1001085 -name: protein-level identification attribute -def: "Protein level information." [PSI:PI] -is_a: MS:1002694 ! single identification result attribute - -[Term] -id: MS:1001086 -name: SEQUEST:sort by XCorr -def: "Sort order of SEQUEST search results by the correlation score." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001087 -name: SEQUEST:ProcessCV -def: "SEQUEST View / Process Input Parameters." [PSI:PI] -is_a: MS:1002096 ! SEQUEST input parameter - -[Term] -id: MS:1001088 -name: protein description -def: "The protein description line from the sequence entry in the source database FASTA file." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001085 ! protein-level identification attribute -is_a: MS:1001342 ! database sequence details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001089 -name: molecule taxonomy -def: "The taxonomy of the resultant molecule from the search." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001085 ! protein-level identification attribute -is_a: MS:1001342 ! database sequence details -is_a: MS:1001512 ! Sequence database filters -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001090 -name: taxonomy nomenclature -def: "OBSOLETE: The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT)." [PSI:PI] -is_a: MS:1001089 ! molecule taxonomy -is_obsolete: true -replaced_by: MS:1001467 -replaced_by: MS:1001468 -replaced_by: MS:1001469 -replaced_by: MS:1001470 - -[Term] -id: MS:1001091 -name: NoEnzyme -is_a: MS:1001045 ! cleavage agent name -comment: This term was made obsolete because it is ambiguous and is replaced by NoCleavage (MS:1001955) and unspecific cleavage (MS:1001956). -is_obsolete: true - -[Term] -id: MS:1001092 -name: peptide sequence-level identification statistic -def: "Identification confidence metric for a peptide." [PSI:PI] -is_a: MS:1001105 ! peptide sequence-level identification attribute - -[Term] -id: MS:1001093 -name: sequence coverage -def: "The percent coverage for the protein based upon the matched peptide sequences (can be calculated)." [PSI:PI] -xref: value-type:xsd\:decimal "The allowed value-type for this CV term." -is_a: MS:1001085 ! protein-level identification attribute -relationship: has_value_type xsd\:decimal ! The allowed value-type for this CV term - -[Term] -id: MS:1001094 -name: SEQUEST:sort by z -def: "Sort order of SEQUEST search results given by the charge." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001041 ! SEQUEST:sortCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001095 -name: SEQUEST:ProcessAll -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001087 ! SEQUEST:ProcessCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001096 -name: SEQUEST:TopPercentMostIntense -def: "Specify \"percentage\" as value of the CVParam." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001087 ! SEQUEST:ProcessCV -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001097 -name: distinct peptide sequences -def: "This counts distinct sequences hitting the protein without regard to a minimal confidence threshold." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1001085 ! protein-level identification attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001098 -name: confident distinct peptide sequences -def: "This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1001085 ! protein-level identification attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001099 -name: confident peptide qualification -def: "The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1001085 ! protein-level identification attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001100 -name: confident peptide sequence number -def: "This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1001085 ! protein-level identification attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001101 -name: protein group or subset relationship -def: "Protein group or subset relationships." [PSI:PI] -is_a: MS:1001085 ! protein-level identification attribute - -[Term] -id: MS:1001102 -name: SEQUEST:Chromatogram -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001006 ! SEQUEST:ViewCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001103 -name: SEQUEST:InfoAndLog -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001006 ! SEQUEST:ViewCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001104 -name: database UniProtKB/Swiss-Prot -def: "The name of the UniProtKB/Swiss-Prot knowledgebase." [PSI:PI] -is_a: MS:1002126 ! database UniProtKB - -[Term] -id: MS:1001105 -name: peptide sequence-level identification attribute -def: "Peptide level information." [PSI:PI] -is_a: MS:1002694 ! single identification result attribute - -[Term] -id: MS:1001106 -name: SEQUEST:TopNumber -def: "Specify \"number\" as value of the CVParam." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1001087 ! SEQUEST:ProcessCV -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001107 -name: data stored in database -def: "Source file for this mzIdentML was a data set in a database." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001108 -name: param: a ion -def: "Parameter information, type of product: a ion with charge on the N-terminal side." [PSI:PI] -is_a: MS:1002473 ! ion series considered in search - -[Term] -id: MS:1001109 -name: SEQUEST:CullTo -def: "Specify cull string as value of the CVParam." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001087 ! SEQUEST:ProcessCV -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001110 -name: SEQUEST:modeCV -def: "SEQUEST Mode Input Parameters." [PSI:PI] -is_a: MS:1002096 ! SEQUEST input parameter - -[Term] -id: MS:1001111 -name: SEQUEST:Full -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001110 ! SEQUEST:modeCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001112 -name: n-terminal flanking residue -def: "Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1003046 ! peptide-to-protein mapping attribute -is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001113 -name: c-terminal flanking residue -def: "Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1003046 ! peptide-to-protein mapping attribute -is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001114 -name: retention time(s) -def: "OBSOLETE Retention time of the spectrum from the source file." [PSI:PI] -comment: This term was made obsolete because scan start time (MS:1000016) should be used instead. -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_units UO:0000010 ! second -relationship: has_units UO:0000031 ! minute -is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001115 -name: scan number(s) -def: "OBSOLETE: use spectrumID attribute of SpectrumIdentificationResult. Take from mzData." [PSI:PI] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1001116 -name: single protein identification statistic -def: "Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group)." [PSI:PI] -is_a: MS:1001085 ! protein-level identification attribute - -[Term] -id: MS:1001117 -name: theoretical mass -def: "The theoretical mass of the molecule (e.g. the peptide sequence and its modifications)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001118 -name: param: b ion -def: "Parameter information, type of product: b ion with charge on the N-terminal side." [PSI:PI] -is_a: MS:1002473 ! ion series considered in search - -[Term] -id: MS:1001119 -name: param: c ion -def: "Parameter information, type of product: c ion with charge on the N-terminal side." [PSI:PI] -is_a: MS:1002473 ! ion series considered in search - -[Term] -id: MS:1001120 -name: SEQUEST:FormatAndLinks -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001110 ! SEQUEST:modeCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001121 -name: number of matched peaks -def: "The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001122 -name: ions series considered -def: "The ion series that were used during the calculation of the count (e.g. a, b, c, d, v, w, x, y, z, a-H2O, a-NH3, b-H2O, b-NH3, y-H2O, y-NH3, b-H20, b+, z-, z+1, z+2, b-H3PO4, y-H3PO4, immonium, internal ya, internal yb)." [PSI:PI] -is_a: MS:1001105 ! peptide sequence-level identification attribute - -[Term] -id: MS:1001123 -name: number of peaks used -def: "The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001124 -name: number of peaks submitted -def: "The number of peaks from the original peaks listed that were submitted to the search engine." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001125 -name: manual validation -def: "Result of quality estimation: decision of a manual validation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001092 ! peptide sequence-level identification statistic -is_a: MS:1001116 ! single protein identification statistic -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001126 -name: SEQUEST:Fast -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001110 ! SEQUEST:modeCV -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001127 -name: peptide sharing details -def: "Accessions Containing Sequence - Accessions for each protein containing this peptide." [PSI:PI] -is_a: MS:1001105 ! peptide sequence-level identification attribute - -[Term] -id: MS:1001128 -name: SEQUEST:selectCV -def: "SEQUEST Select Input Parameters." [PSI:PI] -is_a: MS:1002096 ! SEQUEST input parameter - -[Term] -id: MS:1001129 -name: quantification information -def: "Quantification information." [PSI:PI] -relationship: part_of MS:1001000 ! spectrum interpretation - -[Term] -id: MS:1001130 -name: peptide raw area -def: "OBSOLETE Peptide raw area." [PSI:PI] -comment: This term was made obsolete because it is replaced by 'MS1 feature area' (MS:1001844). -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001131 -name: error on peptide area -def: "Error on peptide area." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001132 -name: peptide ratio -def: "Peptide ratio." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001133 -name: error on peptide ratio -def: "Error on peptide ratio." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001134 -name: protein ratio -def: "Protein ratio." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001135 -name: error on protein ratio -def: "Error on protein ratio." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001136 -name: p-value (protein diff from 1 randomly) -def: "OBSOLETE P-value (protein diff from 1 randomly)." [PSI:PI] -comment: This term was made obsolete because it is replaced by 't-test p-value' (MS:1001855). -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002738 ! protein-level quantification datatype -is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001137 -name: absolute quantity -def: "Absolute quantity in terms of real concentration or molecule copy number in sample." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001138 -name: error on absolute quantity -def: "Error on absolute quantity." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001139 -name: quantitation software name -def: "Quantitation software name." [PSI:PI] -is_a: MS:1000531 ! software -is_a: MS:1001129 ! quantification information - -[Term] -id: MS:1001140 -name: quantitation software version -def: "OBSOLETE Quantitation software version." [PSI:PI] -comment: This term was made obsolete because part of mzQuantML schema. -is_a: MS:1001129 ! quantification information -is_obsolete: true - -[Term] -id: MS:1001141 -name: intensity of precursor ion -def: "The intensity of the precursor ion." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001142 -name: database IPI_human -def: "International Protein Index database for Homo sapiens sequences." [PSI:PI] -is_a: MS:1001013 ! database name - -[Term] -id: MS:1001143 -name: PSM-level search engine specific statistic -def: "Search engine specific peptide spectrum match scores." [PSI:PI] -is_a: MS:1002347 ! PSM-level identification statistic - -[Term] -id: MS:1001144 -name: SEQUEST:SelectDefault -is_a: MS:1001128 ! SEQUEST:selectCV - -[Term] -id: MS:1001145 -name: SEQUEST:SelectAdvancedCV -def: "SEQUEST Select Advanced Input Parameters." [PSI:PI] -is_a: MS:1001128 ! SEQUEST:selectCV - -[Term] -id: MS:1001146 -name: param: a ion-NH3 DEPRECATED -def: "Ion a-NH3 parameter information, type of product: a ion with lost ammonia." [PSI:PI] -is_a: MS:1001066 ! ions series considered in search - -[Term] -id: MS:1001147 -name: protein ambiguity group result details -is_a: MS:1001085 ! protein-level identification attribute -is_a: MS:1001153 ! search engine specific score - -[Term] -id: MS:1001148 -name: param: a ion-H2O DEPRECATED -def: "Ion a-H2O if a significant and fragment includes STED." [PSI:PI] -is_a: MS:1001066 ! ions series considered in search - -[Term] -id: MS:1001149 -name: param: b ion-NH3 DEPRECATED -def: "Ion b-NH3 parameter information, type of product: b ion with lost ammonia." [PSI:PI] -is_a: MS:1001066 ! ions series considered in search - -[Term] -id: MS:1001150 -name: param: b ion-H2O DEPRECATED -def: "Ion b-H2O if b significant and fragment includes STED." [PSI:PI] -is_a: MS:1001066 ! ions series considered in search - -[Term] -id: MS:1001151 -name: param: y ion-NH3 DEPRECATED -def: "Ion y-NH3 parameter information, type of product: y ion with lost ammonia." [PSI:PI] -is_a: MS:1001066 ! ions series considered in search - -[Term] -id: MS:1001152 -name: param: y ion-H2O DEPRECATED -comment: This term was made obsolete - use MS:1001262 and MS:1002455 instead. -is_a: MS:1001066 ! ions series considered in search - -[Term] -id: MS:1001153 -name: search engine specific score -def: "Search engine specific scores." [PSI:PI] -is_a: MS:1002694 ! single identification result attribute - -[Term] -id: MS:1001154 -name: SEQUEST:probability -def: "The SEQUEST result 'Probability'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001155 -name: SEQUEST:xcorr -def: "The SEQUEST result 'XCorr'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001156 -name: SEQUEST:deltacn -def: "The SEQUEST result 'DeltaCn'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001157 -name: SEQUEST:sp -def: "The SEQUEST result 'Sp' (protein)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001158 -name: SEQUEST:Uniq -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001159 -name: SEQUEST:expectation value -def: "The SEQUEST result 'Expectation value'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001153 ! search engine specific score -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001160 -name: SEQUEST:sf -def: "The SEQUEST result 'Sf'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001161 -name: SEQUEST:matched ions -def: "The SEQUEST result 'Matched Ions'." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1001162 -name: SEQUEST:total ions -def: "The SEQUEST result 'Total Ions'." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1001163 -name: SEQUEST:consensus score -def: "The SEQUEST result 'Consensus Score'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001153 ! search engine specific score -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001164 -name: Paragon:unused protscore -def: "The Paragon result 'Unused ProtScore'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001165 -name: Paragon:total protscore -def: "The Paragon result 'Total ProtScore'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001166 -name: Paragon:score -def: "The Paragon result 'Score'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001167 -name: Paragon:confidence -def: "The Paragon result 'Confidence'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001168 -name: Paragon:expression error factor -def: "The Paragon result 'Expression Error Factor'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001169 -name: Paragon:expression change p-value -def: "The Paragon result 'Expression change P-value'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001170 -name: Paragon:contrib -def: "The Paragon result 'Contrib'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001171 -name: Mascot:score -def: "The Mascot result 'Score'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001172 -name: Mascot:expectation value -def: "The Mascot result 'expectation value'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001173 -name: Mascot:matched ions -def: "The Mascot result 'Matched ions'." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001174 -name: Mascot:total ions -def: "The Mascot result 'Total ions'." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001175 -name: peptide shared in multiple proteins -def: "A peptide matching multiple proteins." [PSI:PI] -is_a: MS:1001127 ! peptide sharing details - -[Term] -id: MS:1001176 -name: (?<=[KR])(?\!P) -def: "Regular expression for Trypsin." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001177 -name: number of molecular hypothesis considered -def: "Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1001184 ! search statistics -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001178 -name: database EST -def: "Expressed sequence tag nucleotide sequence database." [PSI:PI] -is_a: MS:1001079 ! database type nucleotide - -[Term] -id: MS:1001180 -name: Cleavage agent regular expression -def: "Regular expressions for cleavage enzymes." [PSI:PI] -relationship: part_of MS:1001044 ! cleavage agent details -is_a: MS:1002479 ! regular expression - -[Term] -id: MS:1001184 -name: search statistics -def: "The details of the actual run of the search." [PSI:PI] -is_a: MS:1001405 ! spectrum identification result details - -[Term] -id: MS:1001189 -name: modification specificity peptide N-term -def: "As parameter for search engine: apply the modification only at the N-terminus of a peptide." [PSI:PI] -is_a: MS:1001056 ! modification specificity rule - -[Term] -id: MS:1001190 -name: modification specificity peptide C-term -def: "As parameter for search engine: apply the modification only at the C-terminus of a peptide." [PSI:PI] -is_a: MS:1001056 ! modification specificity rule - -[Term] -id: MS:1001191 -name: p-value -def: "OBSOLETE Quality estimation by p-value." [PSI:PI] -comment: This term was made obsolete because now is split into peptide and protein terms. -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001092 ! peptide sequence-level identification statistic -is_a: MS:1001198 ! protein identification confidence metric -is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001192 -name: Expect value -def: "Result of quality estimation: Expect value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001092 ! peptide sequence-level identification statistic -is_a: MS:1001116 ! single protein identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001193 -name: confidence score -def: "Result of quality estimation: confidence score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001092 ! peptide sequence-level identification statistic -is_a: MS:1001116 ! single protein identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001194 -name: quality estimation with decoy database -def: "Quality estimation by decoy database." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001060 ! quality estimation method details -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001195 -name: decoy DB type reverse -def: "Decoy type: Amino acids of protein sequences are used in reverse order." [PSI:PI] -is_a: MS:1001450 ! decoy DB details - -[Term] -id: MS:1001196 -name: decoy DB type randomized -def: "Decoy type: Amino acids of protein sequences are randomized (keeping the original protein mass)." [PSI:PI] -is_a: MS:1001450 ! decoy DB details - -[Term] -id: MS:1001197 -name: DB composition target+decoy -def: "Decoy database composition: database contains original (target) and decoy entries." [PSI:PI] -is_a: MS:1001450 ! decoy DB details - -[Term] -id: MS:1001198 -name: protein identification confidence metric -def: "Identification confidence metric for a protein." [PSI:PI] -is_a: MS:1001116 ! single protein identification statistic - -[Term] -id: MS:1001199 -name: Mascot DAT format -def: "Source file for this mzIdentML was in Mascot DAT file format." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001200 -name: SEQUEST out file format -def: "Source file for this mzIdentML was in SEQUEST out file format." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001201 -name: DB MW filter maximum -def: "Maximum value of molecular weight filter." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001512 ! Sequence database filters -relationship: has_units UO:0000221 ! dalton -relationship: has_units UO:0000222 ! kilodalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001202 -name: DB MW filter minimum -def: "Minimum value of molecular weight filter." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001512 ! Sequence database filters -relationship: has_units UO:0000221 ! dalton -relationship: has_units UO:0000222 ! kilodalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001203 -name: DB PI filter maximum -def: "Maximum value of isoelectric point filter." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001512 ! Sequence database filters -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001204 -name: DB PI filter minimum -def: "Minimum value of isoelectric point filter." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001512 ! Sequence database filters -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001207 -name: Mascot -def: "The name of the Mascot search engine." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001208 -name: SEQUEST -def: "The name of the SEQUEST search engine." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001209 -name: Phenyx -def: "The name of the Phenyx search engine." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001210 -name: mass type settings -def: "The type of mass difference value to be considered by the search engine (monoisotopic or average)." [PSI:PI] -is_a: MS:1001249 ! search input details - -[Term] -id: MS:1001211 -name: parent mass type mono -def: "Mass type setting for parent mass was monoisotopic." [PSI:PI] -is_a: MS:1001210 ! mass type settings - -[Term] -id: MS:1001212 -name: parent mass type average -def: "Mass type setting for parent mass was average isotopic." [PSI:PI] -is_a: MS:1001210 ! mass type settings - -[Term] -id: MS:1001213 -name: search result details -def: "OBSOLETE: Scores and global result characteristics." [PSI:PI] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1001214 -name: protein-level global FDR -def: "Estimation of the global false discovery rate of proteins." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002705 ! protein-level result list statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001215 -name: SEQUEST:PeptideSp -def: "The SEQUEST result 'Sp' in out file (peptide)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001217 -name: SEQUEST:PeptideRankSp -def: "The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1001218 -name: SEQUEST:PeptideNumber -def: "The SEQUEST result '#' in out file (peptide)." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1001219 -name: SEQUEST:PeptideIdnumber -def: "The SEQUEST result 'Id#' in out file (peptide)." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1001220 -name: frag: y ion -def: "Fragmentation information, type of product: y ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001221 -name: product ion attribute -def: "Fragmentation information like ion types." [PSI:PI] -is_a: MS:1002694 ! single identification result attribute - -[Term] -id: MS:1001222 -name: frag: b ion - H2O -def: "Fragmentation information, type of product: b ion without water." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001223 -name: frag: y ion - H2O -def: "Fragmentation information, type of product: y ion without water." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001224 -name: frag: b ion -def: "Fragmentation information, type of product: b ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001225 -name: product ion m/z -def: "The m/z of the product ion." [PSI:PI] -synonym: "fragment ion m/z" EXACT [] -is_a: MS:1001221 ! product ion attribute -relationship: has_units MS:1000040 ! m/z - -[Term] -id: MS:1001226 -name: product ion intensity -def: "The intensity of a single product ion." [PSI:PI] -synonym: "fragment ion intensity" EXACT [] -is_a: MS:1001221 ! product ion attribute -relationship: has_units MS:1000131 ! number of detector counts -relationship: has_units MS:1000132 ! percent of base peak -relationship: has_units MS:1000814 ! counts per second -relationship: has_units MS:1000905 ! percent of base peak times 100 - -[Term] -id: MS:1001227 -name: product ion m/z error -def: "The product ion m/z error." [PSI:PI] -is_a: MS:1001221 ! product ion attribute -relationship: has_units MS:1000040 ! m/z -relationship: has_units UO:0000166 ! parts per notation unit - -[Term] -id: MS:1001228 -name: frag: x ion -def: "Fragmentation information, type of product: x ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001229 -name: frag: a ion -def: "Fragmentation information, type of product: a ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001230 -name: frag: z ion -def: "Fragmentation information, type of product: z ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001231 -name: frag: c ion -def: "Fragmentation information, type of product: c ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001232 -name: frag: b ion - NH3 -def: "Ion b-NH3 fragmentation information, type of product: b ion without ammonia." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001233 -name: frag: y ion - NH3 -def: "Ion y-NH3 fragmentation information, type of product: y ion without ammonia." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001234 -name: frag: a ion - H2O -def: "Fragmentation information, type of product: a ion without water." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001235 -name: frag: a ion - NH3 -def: "Ion a-NH3 fragmentation information, type of product: a ion without ammonia." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001236 -name: frag: d ion -def: "Fragmentation information, type of product: d ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001237 -name: frag: v ion -def: "Fragmentation information, type of product: v ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001238 -name: frag: w ion -def: "Fragmentation information, type of product: w ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001239 -name: frag: immonium ion -def: "Fragmentation information, type of product: immonium ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001240 -name: non-identified ion -def: "Non-identified ion." [PSI:PI] -is_a: MS:1001221 ! product ion attribute - -[Term] -id: MS:1001241 -name: co-eluting ion -def: "Co-eluting ion." [PSI:PI] -is_a: MS:1001221 ! product ion attribute - -[Term] -id: MS:1001242 -name: SEQUEST out folder -def: "Source file for this mzIdentML was a SEQUEST folder with its out files." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001243 -name: SEQUEST summary -def: "Source file for this mzIdentML was a SEQUEST summary page (proteins)." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001245 -name: PerSeptive PKS format -def: "PerSeptive peak list file format." [http://www.matrixscience.com/help/data_file_help.html#PKS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1001246 -name: SCIEX API III format -def: "PE SCIEX peak list file format." [http://www.matrixscience.com/help/data_file_help.html#API] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1001247 -name: Bruker XML format -def: "Bruker data exchange XML format." [PSI:PI] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1001249 -name: search input details -def: "Details describing the search input." [PSI:PI] -relationship: part_of MS:1001000 ! spectrum interpretation - -[Term] -id: MS:1001250 -name: local FDR -def: "Result of quality estimation: the local FDR at the current position of a sorted list." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001092 ! peptide sequence-level identification statistic -is_a: MS:1001116 ! single protein identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001251 -name: Trypsin -def: "Enzyme trypsin." [PSI:PI] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001176 ! (?<=[KR])(?!P) - -[Term] -id: MS:1001252 -name: DB source EBI -def: "Database source EBI." [PSI:PI] -is_a: MS:1001012 ! database source - -[Term] -id: MS:1001253 -name: DB source NCBI -def: "Database source NCBI." [PSI:PI] -is_a: MS:1001012 ! database source - -[Term] -id: MS:1001254 -name: DB source UniProt -def: "Database source UniProt." [PSI:PI] -is_a: MS:1001012 ! database source - -[Term] -id: MS:1001255 -name: fragment mass type average -def: "Mass type setting for fragment mass was average isotopic." [PSI:PI] -is_a: MS:1001210 ! mass type settings - -[Term] -id: MS:1001256 -name: fragment mass type mono -def: "Mass type setting for fragment mass was monoisotopic." [PSI:PI] -is_a: MS:1001210 ! mass type settings - -[Term] -id: MS:1001257 -name: param: v ion -def: "Parameter information, type of product: side chain loss v ion." [PSI:PI] -is_a: MS:1002473 ! ion series considered in search - -[Term] -id: MS:1001258 -name: param: d ion -def: "Parameter information, type of product: side chain loss d ion." [PSI:PI] -is_a: MS:1002473 ! ion series considered in search - -[Term] -id: MS:1001259 -name: param: immonium ion -def: "Parameter information, type of product: immonium ion." [PSI:PI] -is_a: MS:1002473 ! ion series considered in search - -[Term] -id: MS:1001260 -name: param: w ion -def: "Parameter information, type of product: side chain loss w ion." [PSI:PI] -is_a: MS:1002473 ! ion series considered in search - -[Term] -id: MS:1001261 -name: param: x ion -def: "Parameter information, type of product: x ion with charge on the C-terminal side." [PSI:PI] -is_a: MS:1002473 ! ion series considered in search - -[Term] -id: MS:1001262 -name: param: y ion -def: "Parameter information, type of product: y ion with charge on the C-terminal side." [PSI:PI] -is_a: MS:1002473 ! ion series considered in search - -[Term] -id: MS:1001263 -name: param: z ion -def: "Parameter information, type of product: z ion with charge on the C-terminal side." [PSI:PI] -is_a: MS:1002473 ! ion series considered in search - -[Term] -id: MS:1001266 -name: role type -def: "Role of a Person or Organization." [PSI:PI] -is_a: MS:1000585 ! contact attribute - -[Term] -id: MS:1001267 -name: software vendor -def: "Software vendor role." [PSI:PI] -is_a: MS:1001266 ! role type - -[Term] -id: MS:1001268 -name: programmer -def: "Programmer role." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001266 ! role type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001269 -name: instrument vendor -def: "Instrument vendor role." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001266 ! role type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001270 -name: lab personnel -def: "Lab personnel role." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001266 ! role type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001271 -name: researcher -def: "Researcher role." [PSI:PI] -is_a: MS:1001266 ! role type - -[Term] -id: MS:1001272 -name: (?<=R)(?\!P) -def: "Regular expression for Arg-C." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001273 -name: (?=[BD]) -def: "Regular expression for Asp-N." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001274 -name: (?=[DE]) -def: "Regular expression for Asp-N-ambic." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001275 -name: ProteinScape SearchEvent -def: "Source data for this mzIdentML was a ProteinScape SearchEvent." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001276 -name: ProteinScape Gel -def: "Source data for this mzIdentML was a ProteinScape Gel." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001283 -name: decoy DB accession regexp -def: "Specify the regular expression for decoy accession numbers." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001450 ! decoy DB details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001284 -name: decoy DB derived from -def: "OBSOLETE The name of the database, the search database was derived from." [PSI:PI] -comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. -is_a: MS:1001450 ! decoy DB details -is_obsolete: true - -[Term] -id: MS:1001285 -name: database IPI_mouse -def: "International Protein Index database for Mus musculus sequences." [PSI:PI] -is_a: MS:1001013 ! database name - -[Term] -id: MS:1001286 -name: database IPI_rat -def: "International Protein Index database for Rattus norvegicus sequences." [PSI:PI] -is_a: MS:1001013 ! database name - -[Term] -id: MS:1001287 -name: database IPI_zebrafish -def: "International Protein Index database for Danio rerio sequences." [PSI:PI] -is_a: MS:1001013 ! database name - -[Term] -id: MS:1001288 -name: database IPI_chicken -def: "International Protein Index database for Gallus gallus sequences." [PSI:PI] -is_a: MS:1001013 ! database name - -[Term] -id: MS:1001289 -name: database IPI_cow -def: "International Protein Index database for Bos taurus sequences." [PSI:PI] -is_a: MS:1001013 ! database name - -[Term] -id: MS:1001290 -name: database IPI_arabidopsis -def: "International Protein Index database for Arabidopsis thaliana sequences." [PSI:PI] -is_a: MS:1001013 ! database name - -[Term] -id: MS:1001291 -name: decoy DB from nr -def: "OBSOLETE Decoy database from a non-redundant GenBank sequence database." [PSI:PI] -comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. -is_obsolete: true - -[Term] -id: MS:1001292 -name: decoy DB from IPI_rat -def: "OBSOLETE Decoy database from a International Protein Index database for Rattus norvegicus." [PSI:PI] -comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. -is_obsolete: true - -[Term] -id: MS:1001293 -name: decoy DB from IPI_mouse -def: "OBSOLETE Decoy database from a International Protein Index database for Mus musculus." [PSI:PI] -comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. -is_obsolete: true - -[Term] -id: MS:1001294 -name: decoy DB from IPI_arabidopsis -def: "OBSOLETE Decoy database from a International Protein Index database for Arabidopsis thaliana." [PSI:PI] -comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. -is_obsolete: true - -[Term] -id: MS:1001295 -name: decoy DB from EST -def: "OBSOLETE Decoy database from an expressed sequence tag nucleotide sequence database." [PSI:PI] -comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. -is_obsolete: true - -[Term] -id: MS:1001296 -name: decoy DB from IPI_zebrafish -def: "OBSOLETE Decoy database from a International Protein Index database for Danio rerio." [PSI:PI] -comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. -is_obsolete: true - -[Term] -id: MS:1001297 -name: decoy DB from UniProtKB/Swiss-Prot -def: "OBSOLETE Decoy database from a Swiss-Prot protein sequence database." [PSI:PI] -comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. -is_obsolete: true - -[Term] -id: MS:1001298 -name: decoy DB from IPI_chicken -def: "OBSOLETE Decoy database from a International Protein Index database for Gallus gallus." [PSI:PI] -comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. -is_obsolete: true - -[Term] -id: MS:1001299 -name: decoy DB from IPI_cow -def: "OBSOLETE Decoy database from a International Protein Index database for Bos taurus." [PSI:PI] -comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. -is_obsolete: true - -[Term] -id: MS:1001300 -name: decoy DB from IPI_human -def: "OBSOLETE Decoy database from a International Protein Index database for Homo sapiens." [PSI:PI] -comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. -is_obsolete: true - -[Term] -id: MS:1001301 -name: protein rank -def: "The rank of the protein in a list sorted by the search engine." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1001085 ! protein-level identification attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001302 -name: search engine specific input parameter -def: "Search engine specific input parameters." [PSI:PI] -is_a: MS:1002093 ! search engine input parameter - -[Term] -id: MS:1001303 -name: Arg-C -def: "Endoproteinase Arg-C." [PSI:PI] -synonym: "Trypsin/R" EXACT [] -synonym: "Clostripain" EXACT [] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001272 ! (?<=R)(?!P) - -[Term] -id: MS:1001304 -name: Asp-N -def: "Endoproteinase Asp-N." [PSI:PI] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001273 ! (?=[BD]) - -[Term] -id: MS:1001305 -name: Asp-N_ambic -def: "Enzyme Asp-N, Ammonium Bicarbonate (AmBic)." [PSI:PI] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001274 ! (?=[DE]) - -[Term] -id: MS:1001306 -name: Chymotrypsin -def: "Enzyme chymotrypsin." [PSI:PI] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001332 ! (?<=[FYWL])(?!P) - -[Term] -id: MS:1001307 -name: CNBr -def: "Cyanogen bromide." [PSI:PI] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001333 ! (?<=M) - -[Term] -id: MS:1001308 -name: Formic_acid -def: "Formic acid." [PubChem_Compound:284] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001334 ! ((?<=D))|((?=D)) - -[Term] -id: MS:1001309 -name: Lys-C -def: "Endoproteinase Lys-C." [PSI:PI] -synonym: "Trypsin/K" EXACT [] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001335 ! (?<=K)(?!P) - -[Term] -id: MS:1001310 -name: Lys-C/P -def: "Proteinase Lys-C/P." [PSI:PI] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001336 ! (?<=K) - -[Term] -id: MS:1001311 -name: PepsinA -def: "PepsinA proteinase." [PSI:PI] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001337 ! (?<=[FL]) - -[Term] -id: MS:1001312 -name: TrypChymo -def: "Cleavage agent TrypChymo." [PSI:PI] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001338 ! (?<=[FYWLKR])(?!P) - -[Term] -id: MS:1001313 -name: Trypsin/P -def: "Cleavage agent Trypsin/P." [PSI:PI] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001339 ! (?<=[KR]) - -[Term] -id: MS:1001314 -name: V8-DE -def: "Cleavage agent V8-DE." [PSI:PI] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001340 ! (?<=[BDEZ])(?!P) - -[Term] -id: MS:1001315 -name: V8-E -def: "Cleavage agent V8-E." [PSI:PI] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001341 ! (?<=[EZ])(?!P) - -[Term] -id: MS:1001316 -name: Mascot:SigThreshold -def: "Significance threshold below which the p-value of a peptide match must lie to be considered statistically significant (default 0.05)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001317 -name: Mascot:MaxProteinHits -def: "The number of protein hits to display in the report. If 'Auto', all protein hits that have a protein score exceeding the average peptide identity threshold are reported. Otherwise an integer at least 1." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001318 -name: Mascot:ProteinScoringMethod -def: "Mascot protein scoring method; either 'Standard' or 'MudPIT'." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001319 -name: Mascot:MinMSMSThreshold -def: "Mascot peptide match ion score threshold. If between 0 and 1, then peptide matches whose expect value exceeds the thresholds are suppressed; if at least 1, then peptide matches whose ion score is below the threshold are suppressed." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001320 -name: Mascot:ShowHomologousProteinsWithSamePeptides -def: "If true, show (sequence or spectrum) same-set proteins. Otherwise they are suppressed." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001321 -name: Mascot:ShowHomologousProteinsWithSubsetOfPeptides -def: "If true, show (sequence or spectrum) sub-set and subsumable proteins. Otherwise they are suppressed." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001322 -name: Mascot:RequireBoldRed -def: "Only used in Peptide Summary and Select Summary reports. If true, a peptide match must be 'bold red' to be included in the report; bold red means the peptide is a top ranking match in a query and appears for the first time (in linear order) in the list of protein hits." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001323 -name: Mascot:UseUnigeneClustering -def: "If true, then the search results are against a nucleic acid database and Unigene clustering is enabled. Otherwise UniGene clustering is not in use." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001324 -name: Mascot:IncludeErrorTolerantMatches -def: "If true, then the search results are error tolerant and peptide matches from the second pass are included in search results. Otherwise no error tolerant peptide matches are included." [http://www.matrixscience.com/help/error_tolerant_help.html] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001325 -name: Mascot:ShowDecoyMatches -def: "If true, then the search results are against an automatically generated decoy database and the reported peptide matches and protein hits come from the decoy database. Otherwise peptide matches and protein hits come from the original database." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001326 -name: add_others -def: "OBSOLETE." [PSI:PI] -comment: This former purgatory term was made obsolete. -is_obsolete: true - -[Term] -id: MS:1001328 -name: OMSSA:evalue -def: "OMSSA E-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001329 -name: OMSSA:pvalue -def: "OMSSA p-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001330 -name: X\!Tandem:expect -def: "The X!Tandem expectation value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001331 -name: X\!Tandem:hyperscore -def: "The X!Tandem hyperscore." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001332 -name: (?<=[FYWL])(?\!P) -def: "Regular expression for Chymotrypsin." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001333 -name: (?<=M) -def: "Regular expression for CNBr." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001334 -name: ((?<=D))|((?=D)) -def: "Regular expression for formic acid." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001335 -name: (?<=K)(?\!P) -def: "Regular expression for Lys-C." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001336 -name: (?<=K) -def: "Regular expression for Lys-C/P." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001337 -name: (?<=[FL]) -def: "Regular expression for PepsinA." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001338 -name: (?<=[FYWLKR])(?\!P) -def: "Regular expression for TrypChymo." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001339 -name: (?<=[KR]) -def: "Regular expression for Trypsin/P." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001340 -name: (?<=[BDEZ])(?\!P) -def: "Regular expression for V8-DE." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001341 -name: (?<=[EZ])(?\!P) -def: "Regular expression for V8-E." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001342 -name: database sequence details -def: "Details about a single database sequence." [PSI:PI] -is_a: MS:1001011 ! search database details - -[Term] -id: MS:1001343 -name: NA sequence -def: "The sequence is a nucleic acid sequence." [PSI:PI] -is_a: MS:1001342 ! database sequence details - -[Term] -id: MS:1001344 -name: AA sequence -def: "The sequence is a amino acid sequence." [PSI:PI] -is_a: MS:1001342 ! database sequence details - -[Term] -id: MS:1001345 -name: mass table source -def: "Children of this term specify the source of the mass table used." [PSI:PI] -is_a: MS:1001354 ! mass table options - -[Term] -id: MS:1001346 -name: AAIndex mass table -def: "The masses used in the mass table are taken from AAIndex." [PSI:PI] -is_a: MS:1001345 ! mass table source - -[Term] -id: MS:1001347 -name: database file formats -def: "The children of this term define file formats of the sequence database used." [PSI:PI] -is_a: MS:1001011 ! search database details - -[Term] -id: MS:1001348 -name: FASTA format -def: "The sequence database was stored in the FASTA format." [PSI:PI] -is_a: MS:1001347 ! database file formats - -[Term] -id: MS:1001349 -name: ASN.1 -def: "The sequence database was stored in the Abstract Syntax Notation 1 format." [PSI:PI] -is_a: MS:1001347 ! database file formats - -[Term] -id: MS:1001350 -name: NCBI *.p* -def: "The sequence database was stored in the NCBI formatdb (*.p*) format." [PSI:PI] -is_a: MS:1001347 ! database file formats - -[Term] -id: MS:1001351 -name: clustal aln -def: "ClustalW ALN (multiple alignment) format." [PSI:PI] -is_a: MS:1001347 ! database file formats - -[Term] -id: MS:1001352 -name: embl em -def: "EMBL entry format." [PSI:PI] -is_a: MS:1001347 ! database file formats - -[Term] -id: MS:1001353 -name: NBRF PIR -def: "The NBRF PIR was used as format." [PSI:PI] -is_a: MS:1001347 ! database file formats - -[Term] -id: MS:1001354 -name: mass table options -def: "Root node for options for the mass table used." [PSI:PI] -relationship: part_of MS:1001000 ! spectrum interpretation - -[Term] -id: MS:1001355 -name: peptide descriptions -def: "Descriptions of peptides." [PSI:PI] -is_a: MS:1001105 ! peptide sequence-level identification attribute - -[Term] -id: MS:1001356 -name: spectrum descriptions -def: "Descriptions of the input spectra." [PSI:PI] -is_a: MS:1001249 ! search input details - -[Term] -id: MS:1001357 -name: spectrum quality descriptions -def: "Description of the quality of the input spectrum." [PSI:PI] -is_a: MS:1001356 ! spectrum descriptions - -[Term] -id: MS:1001358 -name: msmsEval quality -def: "This term reports the quality of the spectrum assigned by msmsEval." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001357 ! spectrum quality descriptions -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001359 -name: ambiguous residues -def: "Children of this term describe ambiguous residues." [PSI:PI] -relationship: part_of MS:1001000 ! spectrum interpretation - -[Term] -id: MS:1001360 -name: alternate single letter codes -def: "List of standard residue one letter codes which are used to replace a non-standard." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001359 ! ambiguous residues -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001361 -name: alternate mass -def: "List of masses a non-standard letter code is replaced with." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001359 ! ambiguous residues -relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001362 -name: number of unmatched peaks -def: "The number of unmatched peaks." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1002345 ! PSM-level attribute -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001363 -name: peptide unique to one protein -def: "A peptide matching only one." [PSI:PI] -is_a: MS:1001127 ! peptide sharing details - -[Term] -id: MS:1001364 -name: peptide sequence-level global FDR -def: "Estimation of the global false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002703 ! peptide sequence-level result list statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001365 -name: frag: internal yb ion -def: "Fragmentation information, type of product: internal yb ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001366 -name: frag: internal ya ion -def: "Fragmentation information, type of product: internal ya ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001367 -name: frag: z+1 ion -def: "Fragmentation information, type of product: z+1 ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001368 -name: frag: z+2 ion -def: "Fragmentation information, type of product: z+2 ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001369 -name: text format -def: "Simple text file format of \"m/z [intensity]\" values for a PMF (or single MS2) search." [PSI:PI] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1001370 -name: Mascot:homology threshold -def: "The Mascot result 'homology threshold'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001371 -name: Mascot:identity threshold -def: "The Mascot result 'identity threshold'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001372 -name: SEQUEST:Sequences -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001373 -name: SEQUEST:TIC -def: "SEQUEST total ion current." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001374 -name: SEQUEST:Sum -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001375 -name: Phenyx:Instrument Type -def: "The instrument type parameter value in Phenyx." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001376 -name: Phenyx:Scoring Model -def: "The selected scoring model in Phenyx." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001377 -name: Phenyx:Default Parent Charge -def: "The default parent charge value in Phenyx." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001378 -name: Phenyx:Trust Parent Charge -def: "The parameter in Phenyx that specifies if the experimental charge state is to be considered as correct." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001379 -name: Phenyx:Turbo -def: "The turbo mode parameter in Phenyx." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001380 -name: Phenyx:Turbo:ErrorTol -def: "The maximal allowed fragment m/z error filter considered in the turbo mode of Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001381 -name: Phenyx:Turbo:Coverage -def: "The minimal peptide sequence coverage value, expressed in percent, considered in the turbo mode of Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001382 -name: Phenyx:Turbo:Series -def: "The list of ion series considered in the turbo mode of Phenyx." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001383 -name: Phenyx:MinPepLength -def: "The minimal number of residues for a peptide to be considered for a valid identification in Phenyx." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001384 -name: Phenyx:MinPepzscore -def: "The minimal peptide z-score for a peptide to be considered for a valid identification in Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001385 -name: Phenyx:MaxPepPvalue -def: "The maximal peptide p-value for a peptide to be considered for a valid identification in Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001386 -name: Phenyx:AC Score -def: "The minimal protein score required for a protein database entry to be displayed in the list of identified proteins in Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001387 -name: Phenyx:Conflict Resolution -def: "The parameter in Phenyx that specifies if the conflict resolution algorithm is to be used." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002097 ! Phenyx input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001388 -name: Phenyx:AC -def: "The primary sequence database identifier of a protein in Phenyx." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001389 -name: Phenyx:ID -xref: value-type:xsd\:string "The allowed value-type for this CV term." -def: "A secondary sequence database identifier of a protein in Phenyx." [PSI:PI] -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001390 -name: Phenyx:Score -def: "The protein score of a protein match in Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001391 -name: Phenyx:Peptides1 -def: "First number of phenyx result \"#Peptides\"." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001392 -name: Phenyx:Peptides2 -def: "Second number of phenyx result \"#Peptides\"." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001393 -name: Phenyx:Auto -def: "The value of the automatic peptide acceptance filter in Phenyx." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001394 -name: Phenyx:User -def: "The value of the user-defined peptide acceptance filter in Phenyx." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001395 -name: Phenyx:Pepzscore -def: "The z-score value of a peptide sequence match in Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001396 -name: Phenyx:PepPvalue -def: "The p-value of a peptide sequence match in Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001397 -name: Phenyx:NumberOfMC -def: "The number of missed cleavages of a peptide sequence in Phenyx." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001398 -name: Phenyx:Modif -def: "The expression of the nature and position(s) of modified residue(s) on a matched peptide sequence in Phenyx." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001399 -name: OMSSA csv format -def: "Source file for this mzIdentML was in OMSSA csv file format." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001400 -name: OMSSA xml format -def: "Source file for this mzIdentML was in OMSSA xml file format." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001401 -name: X\!Tandem xml format -def: "Source file for this mzIdentML was in X!Tandem xml file format." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001405 -name: spectrum identification result details -def: "This subsection describes terms which can describe details of spectrum identification results." [PSI:PI] -relationship: part_of MS:1001000 ! spectrum interpretation - -[Term] -id: MS:1001406 -name: param: internal yb ion -def: "Parameter information, type of product: internal yb ion." [PSI:PI] -is_a: MS:1002473 ! ion series considered in search - -[Term] -id: MS:1001407 -name: param: internal ya ion -def: "Parameter information, type of product: internal ya ion." [PSI:PI] -is_a: MS:1002473 ! ion series considered in search - -[Term] -id: MS:1001408 -name: param: z+1 ion -def: "Parameter information, type of product: z+1 ion." [PSI:PI] -is_a: MS:1002473 ! ion series considered in search - -[Term] -id: MS:1001409 -name: param: z+2 ion -def: "Parameter information, type of product: z+2 ion." [PSI:PI] -is_a: MS:1002473 ! ion series considered in search - -[Term] -id: MS:1001410 -name: translation start codons -def: "The translation start codons used to translate the nucleotides to amino acids." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001411 -name: search tolerance specification -def: "Specification of the search tolerance." [PSI:PI] -is_a: MS:1001249 ! search input details - -[Term] -id: MS:1001412 -name: search tolerance plus value -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001411 ! search tolerance specification -relationship: has_units UO:0000166 ! parts per notation unit -relationship: has_units UO:0000169 ! parts per million -relationship: has_units UO:0000187 ! percent -relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001413 -name: search tolerance minus value -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001411 ! search tolerance specification -relationship: has_units UO:0000166 ! parts per notation unit -relationship: has_units UO:0000169 ! parts per million -relationship: has_units UO:0000187 ! percent -relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001414 -name: MGF scans -def: "OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001405 ! spectrum identification result details -is_obsolete: true -replaced_by: MS:1000797 -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001415 -name: MGF raw scans -def: "OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001405 ! spectrum identification result details -is_obsolete: true -replaced_by: MS:1000798 -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001416 -name: spectrum title -def: "OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001405 ! spectrum identification result details -is_obsolete: true -replaced_by: MS:1000796 -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001417 -name: SpectraST:dot -def: "SpectraST dot product of two spectra, measuring spectral similarity." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001418 -name: SpectraST:dot_bias -def: "SpectraST measure of how much of the dot product is dominated by a few peaks." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001419 -name: SpectraST:discriminant score F -def: "SpectraST spectrum score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001420 -name: SpectraST:delta -def: "SpectraST normalised difference between dot product of top hit and runner-up." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001421 -name: pepXML format -def: "The XML-based pepXML file format for encoding PSM information, created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001422 -name: protXML format -def: "The XML-based protXML file format for encoding protein identifications, created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001423 -name: translation table description -def: "A URL that describes the translation table used to translate the nucleotides to amino acids." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." -is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term - -[Term] -id: MS:1001424 -name: ProteinExtractor:Methodname -def: "Name of the used method in the ProteinExtractor algorithm." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001425 -name: ProteinExtractor:GenerateNonRedundant -def: "Flag indicating if a non redundant scoring should be generated." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001426 -name: ProteinExtractor:IncludeIdentified -def: "Flag indicating if identified proteins should be included." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001427 -name: ProteinExtractor:MaxNumberOfProteins -def: "The maximum number of proteins to consider." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001428 -name: ProteinExtractor:MaxProteinMass -def: "The maximum considered mass for a protein." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001429 -name: ProteinExtractor:MinNumberOfPeptides -def: "The minimum number of proteins to consider." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001430 -name: ProteinExtractor:UseMascot -def: "Flag indicating to include Mascot scoring for calculation of the ProteinExtractor meta score." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001431 -name: ProteinExtractor:MascotPeptideScoreThreshold -def: "Only peptides with scores higher than that threshold are taken into account in Mascot scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001432 -name: ProteinExtractor:MascotUniqueScore -def: "In the final result each protein must have at least one peptide above this Mascot score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001433 -name: ProteinExtractor:MascotUseIdentityScore -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001434 -name: ProteinExtractor:MascotWeighting -def: "Influence of Mascot search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001435 -name: ProteinExtractor:UseSequest -def: "Flag indicating to include SEQUEST scoring for calculation of the ProteinExtractor meta score." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001436 -name: ProteinExtractor:SequestPeptideScoreThreshold -def: "Only peptides with scores higher than that threshold are taken into account in SEQUEST scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001437 -name: ProteinExtractor:SequestUniqueScore -def: "In the final result each protein must have at least one peptide above this SEQUEST score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001438 -name: ProteinExtractor:SequestWeighting -def: "Influence of SEQUEST search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001439 -name: ProteinExtractor:UseProteinSolver -def: "Flag indicating to include ProteinSolver scoring for calculation of the ProteinExtractor meta score." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001440 -name: ProteinExtractor:ProteinSolverPeptideScoreThreshold -def: "Only peptides with scores higher than that threshold are taken into account in ProteinSolver scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001441 -name: ProteinExtractor:ProteinSolverUniqueScore -def: "In the final result each protein must have at least one peptide above this ProteinSolver score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001442 -name: ProteinExtractor:ProteinSolverWeighting -def: "Influence of ProteinSolver search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001443 -name: ProteinExtractor:UsePhenyx -def: "Flag indicating to include Phenyx scoring for calculation of the ProteinExtractor meta score." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001444 -name: ProteinExtractor:PhenyxPeptideScoreThreshold -def: "Only peptides with scores higher than that threshold are taken into account in Phenyx scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001445 -name: ProteinExtractor:PhenyxUniqueScore -def: "In the final result each protein must have at least one peptide above this Phenyx score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001446 -name: ProteinExtractor:PhenyxWeighting -def: "Influence of Phenyx search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001447 -name: prot:FDR threshold -def: "False-discovery rate threshold for proteins." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002485 ! protein-level statistical threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001448 -name: pep:FDR threshold -def: "False-discovery rate threshold for peptides." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002484 ! peptide-level statistical threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001449 -name: OMSSA e-value threshold -def: "Threshold for OMSSA e-value for quality estimation." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002099 ! OMSSA input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001450 -name: decoy DB details -def: "Details of decoy generation and database structure." [PSI:PI] -is_a: MS:1001011 ! search database details - -[Term] -id: MS:1001451 -name: decoy DB generation algorithm -def: "Name of algorithm used for decoy generation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001450 ! decoy DB details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001452 -name: decoy DB type shuffle -def: "Decoy type: Amino acids of protein sequences are used in a random order." [PSI:PI] -is_a: MS:1001450 ! decoy DB details - -[Term] -id: MS:1001453 -name: DB composition only decoy -def: "Decoy database composition: database contains only decoy entries." [PSI:PI] -is_a: MS:1001450 ! decoy DB details - -[Term] -id: MS:1001454 -name: quality estimation with implicite decoy sequences -def: "Decoy entries are generated during the search, not explicitly stored in a database (like Mascot Decoy)." [PSI:PI] -is_a: MS:1001060 ! quality estimation method details - -[Term] -id: MS:1001455 -name: acquisition software -def: "Acquisition software." [PSI:MS] -is_a: MS:1000531 ! software - -[Term] -id: MS:1001456 -name: analysis software -def: "Analysis software." [PSI:MS] -is_a: MS:1000531 ! software - -[Term] -id: MS:1001457 -name: data processing software -def: "Data processing software." [PSI:MS] -is_a: MS:1000531 ! software - -[Term] -id: MS:1001458 -name: spectrum generation information -def: "Vocabularies describing the spectrum generation information." [PSI:PI] -relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies - -[Term] -id: MS:1001459 -name: file format -def: "Format of data files." [PSI:MS] -relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies - -[Term] -id: MS:1001460 -name: unknown modification -def: "This term should be given if the modification was unknown." [PSI:PI] -is_a: MS:1001471 ! peptide modification details - -[Term] -id: MS:1001461 -name: greylag -def: "Greylag identification software." [http://greylag.org/] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001462 -name: PEFF format -def: "The sequence database was stored in the PEFF (PSI enhanced FastA file) format." [PSI:PI] -is_a: MS:1001347 ! database file formats - -[Term] -id: MS:1001463 -name: Phenyx XML format -def: "Phenyx open XML file format." [PSI:PI] -is_a: MS:1000560 ! mass spectrometer file format -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001464 -name: DTASelect format -def: "DTASelect file format." [PMID:12643522, http://www.scripps.edu/cravatt/protomap/dtaselect_instructions.html] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001466 -name: MS2 format -def: "MS2 file format for MS2 spectral data." [PMID:15317041, DOI:10.1002/rcm.1603, http://fields.scripps.edu/sequest/SQTFormat.html] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1001467 -name: taxonomy: NCBI TaxID -def: "This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1001089 ! molecule taxonomy -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001468 -name: taxonomy: common name -def: "This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001089 ! molecule taxonomy -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001469 -name: taxonomy: scientific name -def: "This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001089 ! molecule taxonomy -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001470 -name: taxonomy: Swiss-Prot ID -def: "This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001089 ! molecule taxonomy -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001471 -name: peptide modification details -def: "The children of this term can be used to describe modifications." [PSI:PI] -relationship: part_of MS:1001000 ! spectrum interpretation - -[Term] -id: MS:1001472 -name: selected ion monitoring chromatogram -def: "Representation of an array of the measurements of a selectively monitored ion versus time." [PSI:MS] -synonym: "SIM chromatogram" EXACT [] -is_a: MS:1000810 ! ion current chromatogram - -[Term] -id: MS:1001473 -name: selected reaction monitoring chromatogram -def: "Representation of an array of the measurements of a selectively monitored reaction versus time." [PSI:MS] -synonym: "SRM chromatogram" EXACT [] -is_a: MS:1000810 ! ion current chromatogram - -[Term] -id: MS:1001474 -name: consecutive reaction monitoring chromatogram -def: "OBSOLETE Representation of an array of the measurements of a series of monitored reactions versus time." [PSI:MS] -comment: This term was made obsolete because, by design, it can't be properly represented in mzML 1.1. CRM experiments must be represented in a spectrum-centric way. -synonym: "CRM chromatogram" EXACT [] -is_a: MS:1000810 ! ion current chromatogram -is_obsolete: true - -[Term] -id: MS:1001475 -name: OMSSA -def: "Open Mass Spectrometry Search Algorithm was used to analyze the spectra." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001476 -name: X\!Tandem -def: "X!Tandem was used to analyze the spectra." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001477 -name: SpectraST -def: "SpectraST was used to analyze the spectra." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001478 -name: Mascot Parser -def: "Mascot Parser was used to analyze the spectra." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001479 -name: null-terminated ASCII string -def: "Sequence of zero or more non-zero ASCII characters terminated by a single null (0) byte." [PSI:MS] -is_a: MS:1000518 ! binary data type - -[Term] -id: MS:1001480 -name: SCIEX TOF/TOF nativeID format -def: "Native format defined by jobRun=xsd:nonNegativeInteger spotLabel=xsd:string spectrum=xsd:nonNegativeInteger." [PSI:MS] -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1001481 -name: SCIEX TOF/TOF database -def: "Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument database." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1001482 -name: 5800 TOF/TOF -def: "SCIEX 5800 TOF-TOF Analyzer." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1001483 -name: SCIEX TOF/TOF Series Explorer Software -def: "SCIEX or Applied Biosystems software for TOF/TOF data acquisition and analysis." [PSI:MS] -is_a: MS:1000690 ! SCIEX software -is_a: MS:1001455 ! acquisition software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1001484 -name: intensity normalization -def: "Normalization of data point intensities." [PSI:MS] -is_a: MS:1000543 ! data processing action - -[Term] -id: MS:1001485 -name: m/z calibration -def: "Calibration of data point m/z positions." [PSI:MS] -is_a: MS:1000543 ! data processing action - -[Term] -id: MS:1001486 -name: data filtering -def: "Filtering out part of the data." [PSI:MS] -is_a: MS:1000543 ! data processing action - -[Term] -id: MS:1001487 -name: ProteinExtractor -def: "An algorithm for protein determination/assembly integrated into Bruker's ProteinScape." [PSI:MS] -is_a: MS:1000692 ! Bruker software -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001488 -name: Mascot Distiller -def: "Mascot Distiller." [PSI:PI] -is_a: MS:1001139 ! quantitation software name -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001489 -name: Mascot Integra -def: "Mascot Integra." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001490 -name: Percolator -def: "Percolator." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001491 -name: percolator:Q value -def: "Percolator:Q value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001492 -name: percolator:score -def: "Percolator:score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001493 -name: percolator:PEP -def: "Posterior error probability." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001494 -name: no threshold -def: "In case no threshold was used." [PSI:PI] -is_a: MS:1002482 ! statistical threshold - -[Term] -id: MS:1001495 -name: ProteinScape:SearchResultId -def: "The SearchResultId of this peptide as SearchResult in the ProteinScape database." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001496 -name: ProteinScape:SearchEventId -def: "The SearchEventId of the SearchEvent in the ProteinScape database." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001497 -name: ProteinScape:ProfoundProbability -def: "The Profound probability score stored by ProteinScape." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001498 -name: Profound:z value -def: "The Profound z value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001499 -name: Profound:Cluster -def: "The Profound cluster score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001500 -name: Profound:ClusterRank -def: "The Profound cluster rank." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001501 -name: MSFit:Mowse score -def: "The MSFit Mowse score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001502 -name: Sonar:Score -def: "The Sonar score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001503 -name: ProteinScape:PFFSolverExp -def: "The ProteinSolver exp value stored by ProteinScape." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001504 -name: ProteinScape:PFFSolverScore -def: "The ProteinSolver score stored by ProteinScape." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001505 -name: ProteinScape:IntensityCoverage -def: "The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001506 -name: ProteinScape:SequestMetaScore -def: "The SEQUEST meta score calculated by ProteinScape from the original SEQUEST scores." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001507 -name: ProteinExtractor:Score -def: "The score calculated by ProteinExtractor." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001508 -name: Agilent MassHunter nativeID format -def: "Native format defined by scanId=xsd:nonNegativeInteger." [PSI:PI] -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1001509 -name: Agilent MassHunter format -def: "A data file format found in an Agilent MassHunter directory which contains raw data acquired by an Agilent mass spectrometer." [PSI:PI] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1001510 -name: TSQ Vantage -def: "TSQ Vantage." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1001511 -name: Sequence database filter types -def: "Filter types which are used to filter a sequence database." [PSI:PI] -is_a: MS:1001019 ! database filtering - -[Term] -id: MS:1001512 -name: Sequence database filters -def: "Sequence database filters which actually can contains values, e.g. to limit PI value of the sequences used to search." [PSI:PI] -is_a: MS:1001019 ! database filtering - -[Term] -id: MS:1001513 -name: DB sequence filter pattern -def: "DB sequence filter pattern." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001512 ! Sequence database filters -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001514 -name: DB accession filter string -def: "DB accession filter string." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001512 ! Sequence database filters -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001515 -name: frag: c ion - H2O -def: "Fragmentation information, type of product: c ion without water." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001516 -name: frag: c ion - NH3 -def: "Fragmentation information, type of product: c ion without ammonia." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001517 -name: frag: z ion - H2O -def: "Fragmentation information, type of product: z ion without water." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001518 -name: frag: z ion - NH3 -def: "Fragmentation information, type of product: z ion without ammonia." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001519 -name: frag: x ion - H2O -def: "Fragmentation information, type of product: x ion without water." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001520 -name: frag: x ion - NH3 -def: "Fragmentation information, type of product: x ion without ammonia." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001521 -name: frag: precursor ion - H2O -def: "Fragmentation information, type of product: precursor ion without water." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001522 -name: frag: precursor ion - NH3 -def: "Fragmentation information, type of product: precursor ion without ammonia." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001523 -name: frag: precursor ion -def: "Fragmentation information, type of product: precursor ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1001524 -name: fragment neutral loss -def: "This term can describe a neutral loss m/z value that is lost from an ion." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001471 ! peptide modification details -relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001525 -name: precursor neutral loss -def: "This term can describe a neutral loss m/z value that is lost from an ion." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001471 ! peptide modification details -relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001526 -name: spectrum from database integer nativeID format -def: "Native format defined by databasekey=xsd:long." [PSI:MS] -comment: A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1001527 -name: Proteinscape spectra -def: "Spectra from Bruker/Protagen Proteinscape database." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1001528 -name: Mascot query number -def: "Native format defined by query=xsd:nonNegativeInteger." [PSI:MS] -comment: The spectrum (query) number in a Mascot results file, starting from 1. -is_a: MS:1000767 ! native spectrum identifier format -is_a: MS:1001405 ! spectrum identification result details - -[Term] -id: MS:1001529 -name: spectra data details -def: "Child-terms contain information to map the results back to spectra." [PSI:MS] -is_a: MS:1001249 ! search input details - -[Term] -id: MS:1001530 -name: mzML unique identifier -def: "Native format defined by mzMLid=xsd:IDREF." [PSI:MS] -comment: A unique identifier of a spectrum stored in an mzML file. -is_a: MS:1001529 ! spectra data details - -[Term] -id: MS:1001531 -name: spectrum from ProteinScape database nativeID format -def: "Native format defined by databasekey=xsd:long." [PSI:MS] -comment: A unique identifier of a spectrum stored in a ProteinScape database. -is_a: MS:1000767 ! native spectrum identifier format -is_a: MS:1001529 ! spectra data details - -[Term] -id: MS:1001532 -name: spectrum from database string nativeID format -def: "Native format defined by databasekey=xsd:string." [PSI:MS] -comment: A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). -is_a: MS:1000767 ! native spectrum identifier format -is_a: MS:1001529 ! spectra data details - -[Term] -id: MS:1001533 -name: Bruker Daltonics esquire series -def: "Bruker Daltonics' esquire series." [PSI:MS] -is_a: MS:1000122 ! Bruker Daltonics instrument model - -[Term] -id: MS:1001534 -name: Bruker Daltonics flex series -def: "Bruker Daltonics' flex series." [PSI:MS] -is_a: MS:1000122 ! Bruker Daltonics instrument model - -[Term] -id: MS:1001535 -name: Bruker Daltonics BioTOF series -def: "Bruker Daltonics' BioTOF series." [PSI:MS] -is_a: MS:1000122 ! Bruker Daltonics instrument model - -[Term] -id: MS:1001536 -name: Bruker Daltonics micrOTOF series -def: "Bruker Daltonics' micrOTOF series." [PSI:MS] -is_a: MS:1000122 ! Bruker Daltonics instrument model - -[Term] -id: MS:1001537 -name: BioTOF -def: "Bruker Daltonics' BioTOF: ESI TOF." [PSI:MS] -is_a: MS:1001535 ! Bruker Daltonics BioTOF series - -[Term] -id: MS:1001538 -name: BioTOF III -def: "Bruker Daltonics' BioTOF III: ESI TOF." [PSI:MS] -is_a: MS:1001535 ! Bruker Daltonics BioTOF series - -[Term] -id: MS:1001539 -name: UltroTOF-Q -def: "Bruker Daltonics' UltroTOF-Q: ESI Q-TOF (MALDI optional)." [PSI:MS] -is_a: MS:1001535 ! Bruker Daltonics BioTOF series - -[Term] -id: MS:1001540 -name: micrOTOF II -def: "Bruker Daltonics' micrOTOF II: ESI TOF, Nanospray, APCI, APPI." [PSI:MS] -is_a: MS:1001536 ! Bruker Daltonics micrOTOF series - -[Term] -id: MS:1001541 -name: maXis -def: "Bruker Daltonics' maXis: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] -is_a: MS:1001547 ! Bruker Daltonics maXis series - -[Term] -id: MS:1001542 -name: amaZon ETD -def: "Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR." [PSI:MS] -is_a: MS:1001545 ! Bruker Daltonics amaZon series - -[Term] -id: MS:1001543 -name: microflex LRF -def: "Bruker Daltonics' microflex LRF: MALDI TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1001544 -name: ultrafleXtreme -def: "Bruker Daltonics' ultrafleXtreme: MALDI TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1001545 -name: Bruker Daltonics amaZon series -def: "Bruker Daltonics' amaZon series." [PSI:MS] -is_a: MS:1000122 ! Bruker Daltonics instrument model - -[Term] -id: MS:1001546 -name: amaZon X -def: "Bruker Daltonics' amaZon X: ESI quadrupole ion trap, APCI, APPI, ETD, PTR." [PSI:MS] -is_a: MS:1001545 ! Bruker Daltonics amaZon series - -[Term] -id: MS:1001547 -name: Bruker Daltonics maXis series -def: "Bruker Daltonics' maXis series." [PSI:MS] -is_a: MS:1000122 ! Bruker Daltonics instrument model - -[Term] -id: MS:1001548 -name: Bruker Daltonics solarix series -def: "Bruker Daltonics' solarix: ESI quadrupole ion trap, APCI, APPI, ETD, PTR." [PSI:MS] -is_a: MS:1000122 ! Bruker Daltonics instrument model - -[Term] -id: MS:1001549 -name: solariX -def: "Bruker Daltonics' solariX: ESI, MALDI, Qh-FT_ICR." [PSI:MS] -is_a: MS:1001548 ! Bruker Daltonics solarix series - -[Term] -id: MS:1001550 -name: microflex II -def: "Bruker Daltonics' microflex II: MALDI TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1001553 -name: autoflex II TOF/TOF -def: "Bruker Daltonics' autoflex II TOF/TOF: MALDI TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1001554 -name: autoflex III TOF/TOF smartbeam -def: "Bruker Daltonics' autoflex III TOF/TOF smartbeam: MALDI TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1001555 -name: autoflex -def: "Bruker Daltonics' autoflex: MALDI TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1001556 -name: Bruker Daltonics apex series -def: "Bruker Daltonics' apex series." [PSI:MS] -is_a: MS:1000122 ! Bruker Daltonics instrument model - -[Term] -id: MS:1001557 -name: Shimadzu Corporation software -def: "Shimadzu Corporation software." [PSI:MS] -is_a: MS:1000531 ! software - -[Term] -id: MS:1001558 -name: MALDI Solutions -def: "Shimadzu Biotech software for data acquisition, processing, and analysis." [PSI:MS] -is_a: MS:1001455 ! acquisition software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software -is_a: MS:1001557 ! Shimadzu Corporation software - -[Term] -id: MS:1001559 -name: SCIEX TOF/TOF T2D nativeID format -def: "Native format defined by file=xsd:IDREF." [PSI:MS] -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1001560 -name: SCIEX TOF/TOF T2D format -def: "Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument export format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1001561 -name: Scaffold -def: "Scaffold analysis software." [http://www.proteomesoftware.com] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001562 -name: Scaffold nativeID format -def: "Scaffold native ID format." [PSI:MS] -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1001563 -name: SEQUEST SQT format -def: "Source file for this mzIdentML was in SEQUEST SQT format." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001564 -name: Discoverer MSF format -def: "Source file for this mzIdentML was in Thermo Scientific Discoverer MSF format." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001565 -name: IdentityE XML format -def: "Source file for this mzIdentML was in Waters IdentityE XML format." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001566 -name: ProteinLynx XML format -def: "Source file for this mzIdentML was in Waters ProteinLynx XML format." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001567 -name: SpectrumMill directories -def: "Source file for this mzIdentML was in Agilent SpectrumMill directory format." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1001568 -name: Scaffold:Peptide Probability -def: "Scaffold peptide probability score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001569 -name: IdentityE Score -def: "Waters IdentityE peptide score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001570 -name: ProteinLynx:Log Likelihood -def: "ProteinLynx log likelihood score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001571 -name: ProteinLynx:Ladder Score -def: "Waters ProteinLynx Ladder score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001572 -name: SpectrumMill:Score -def: "Spectrum mill peptide score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001573 -name: SpectrumMill:SPI -def: "SpectrumMill SPI score (%)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001574 -name: report only spectra assigned to identified proteins -def: "Flag indicating to report only the spectra assigned to identified proteins." [PSI:PI] -is_a: MS:1001060 ! quality estimation method details - -[Term] -id: MS:1001575 -name: Scaffold: Minimum Peptide Count -def: "Minimum number of peptides a protein must have to be accepted." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1002106 ! Scaffold input parameter -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001576 -name: Scaffold: Minimum Protein Probability -def: "Minimum protein probability a protein must have to be accepted." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002106 ! Scaffold input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001577 -name: Scaffold: Minimum Peptide Probability -def: "Minimum probability a peptide must have to be accepted for protein scoring." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002106 ! Scaffold input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001578 -name: minimum number of enzymatic termini -def: "Minimum number of enzymatic termini a peptide must have to be accepted." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1002094 ! common search engine input parameter -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001579 -name: Scaffold:Protein Probability -def: "Scaffold protein probability score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001580 -name: SpectrumMill:Discriminant Score -def: "Discriminant score from Agilent SpectrumMill software." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001581 -name: FAIMS compensation voltage -def: "The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -synonym: "FAIMS CV" EXACT [] -is_a: MS:1002892 ! ion mobility attribute -relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001582 -name: XCMS -def: "Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data." [PSI:MS] -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1001583 -name: MaxQuant -def: "MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data." [PSI:MS] -is_a: MS:1001139 ! quantitation software name -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001584 -name: combined pmf + ms-ms search -def: "Search that includes data from Peptide Mass Fingerprint (PMF) and MS2 (aka Peptide Fragment Fingerprint - PFF)." [PSI:MS] -is_a: MS:1001080 ! search type - -[Term] -id: MS:1001585 -name: MyriMatch -def: "Tabb Lab software for directly comparing peptides in a database to tandem mass spectra." [PSI:MS] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001586 -name: DirecTag -def: "Tabb Lab software for generating sequence tags from tandem mass spectra." [PSI:MS] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001587 -name: TagRecon -def: "Tabb Lab software for reconciling sequence tags to a protein database." [PSI:MS] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001588 -name: Pepitome -def: "Tabb Lab software for spectral library searches on tandem mass spectra." [PSI:MS] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001589 -name: MyriMatch:MVH -def: "Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance." [PSI:MS] -synonym: "Pepitome:MVH" EXACT [] -synonym: "TagRecon:MVH" EXACT [] -is_a: MS:1001143 ! PSM-level search engine specific statistic - -[Term] -id: MS:1001590 -name: MyriMatch:mzFidelity -def: "The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution." [PSI:MS] -synonym: "Pepitome:mzFidelity" EXACT [] -synonym: "TagRecon:mzFidelity" EXACT [] -is_a: MS:1001143 ! PSM-level search engine specific statistic - -[Term] -id: MS:1001591 -name: anchor protein -def: "A representative protein selected from a set of sequence same-set or spectrum same-set proteins." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001592 -name: family member protein -def: "A protein with significant homology to another protein, but some distinguishing peptide matches." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001593 -name: group member with undefined relationship OR ortholog protein -def: "TO ENDETAIL: a really generic relationship OR ortholog protein." [PSI:MS] -is_a: MS:1001101 ! protein group or subset relationship - -[Term] -id: MS:1001594 -name: sequence same-set protein -def: "A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001595 -name: spectrum same-set protein -def: "A protein which is indistinguishable or equivalent to another protein, having matches to a set of peptide sequences that cannot be distinguished using the evidence in the mass spectra." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001596 -name: sequence sub-set protein -def: "A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001597 -name: spectrum sub-set protein -def: "A protein with a sub-set of the matched spectra for another protein, where the matches cannot be distinguished using the evidence in the mass spectra, and no distinguishing peptide matches." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001598 -name: sequence subsumable protein -def: "A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001599 -name: spectrum subsumable protein -def: "A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001600 -name: protein inference confidence category -def: "Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable)." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001601 -name: ProteomeDiscoverer:Spectrum Files:Raw File names -def: "OBSOLETE Name and location of the .raw file or files." [PSI:MS] -comment: This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001602 -name: ProteomeDiscoverer:SRF File Selector:SRF File Path -def: "OBSOLETE Path and name of the .srf (SEQUEST Result Format) file." [PSI:MS] -comment: This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001603 -name: ProteomeDiscoverer:Spectrum Selector:Ionization Source -def: "OBSOLETE Ionization source (electro-, nano-, thermospray, electron impact, APCI, MALDI, FAB etc)." [PSI:MS] -comment: This term was made obsolete because it's recommended to use one of the 'inlet type' (MS:1000007) or 'ionization type' (MS:1000008) terms instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001604 -name: ProteomeDiscoverer:Activation Type -def: "OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any)." [PSI:MS] -comment: This term was made obsolete because it's recommended to use one of the 'ionization type' terms (MS:1000008) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001605 -name: ProteomeDiscoverer:Spectrum Selector:Lower RT Limit -def: "Lower retention-time limit." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001606 -name: ProteomeDiscoverer:Mass Analyzer -def: "OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, SectorMS)." [PSI:MS] -comment: This term was made obsolete because it's recommended to use mass analyzer type (MS:1000443) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001607 -name: ProteomeDiscoverer:Max Precursor Mass -def: "Maximum mass limit of a singly charged precursor ion." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001608 -name: ProteomeDiscoverer:Min Precursor Mass -def: "Minimum mass limit of a singly charged precursor ion." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001609 -name: ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count -def: "Minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001610 -name: ProteomeDiscoverer:MS Order -def: "OBSOLETE Level of the mass spectrum (MS2 ... MS10)." [PSI:MS] -comment: This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579) or MSn spectrum (MS:1000580) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001611 -name: ProteomeDiscoverer:Polarity Mode -def: "OBSOLETE Polarity mode (positive or negative)." [PSI:MS] -comment: This term was made obsolete because it's recommended to use scan polarity (MS:1000465) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001612 -name: ProteomeDiscoverer:Spectrum Selector:Precursor Selection -def: "Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3)." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001613 -name: ProteomeDiscoverer:SN Threshold -def: "Signal-to-Noise ratio below which peaks are removed." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001614 -name: ProteomeDiscoverer:Scan Type -def: "OBSOLETE Scan type for the precursor ion (full, Single Ion Monitoring (SIM), Single Reaction Monitoring (SRM))." [PSI:MS] -comment: This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579), MSn spectrum (MS:1000580), CRM spectrum (MS:1000581), SIM spectrum (MS:1000582) or SRM spectrum (MS:1000583) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001615 -name: ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold -def: "Used to filter out tandem mass spectra that have a total intensity current(sum of the intensities of all peaks in a spectrum) below the specified value." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001616 -name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements -def: "Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001617 -name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements -def: "Specifies the charge state of the precursor ions, if it is not defined in the scan header." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001618 -name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements -def: "Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001619 -name: ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements -def: "Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001620 -name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements -def: "Specifies the polarity of the ions monitored if it is not included in the scan header." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001621 -name: ProteomeDiscoverer:Spectrum Selector:Upper RT Limit -def: "Upper retention-time limit." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001622 -name: ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset -def: "Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001623 -name: ProteomeDiscoverer:Non-Fragment Filter:Maximum Neutral Loss Mass -def: "Maximum allowed mass of a neutral loss." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001624 -name: ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor -def: "Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001625 -name: ProteomeDiscoverer:Non-Fragment Filter:Remove Neutral Loss Peaks -def: "Determines whether neutral loss peaks are removed from ETD and ECD spectra." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001626 -name: ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses -def: "Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001627 -name: ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones -def: "Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001628 -name: ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak -def: "Determines whether precursor artifact peaks from the MS2 input spectra are removed." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001629 -name: ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch -def: "Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001630 -name: ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch -def: "Determines whether spectra from different MS order scans can be grouped together." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001631 -name: ProteomeDiscoverer:Spectrum Grouper:Max RT Difference -def: "OBSOLETE Chromatographic window where precursors to be grouped must reside to be considered the same species." [PSI:MS] -comment: This term was made obsolete because it's recommended to use retention time window width (MS:1001907) instead. -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001632 -name: ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion -def: "Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001633 -name: ProteomeDiscoverer:Xtract:Highest Charge -def: "Highest charge state that is allowed for the deconvolution of multiply charged data." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001634 -name: ProteomeDiscoverer:Xtract:Highest MZ -def: "OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract." [PSI:MS] -comment: This term was made obsolete because it's recommended to use scan window upper limit (MS:1000500) instead. -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001635 -name: ProteomeDiscoverer:Xtract:Lowest Charge -def: "Lowest charge state that is allowed for the deconvolution of multiply charged data." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001636 -name: ProteomeDiscoverer:Xtract:Lowest MZ -def: "OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract." [PSI:MS] -comment: This term was made obsolete because it's recommended to use scan window lower limit (MS:1000501) instead. -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001637 -name: ProteomeDiscoverer:Xtract:Monoisotopic Mass Only -def: "Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001638 -name: ProteomeDiscoverer:Xtract:Overlapping Remainder -def: "Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted)." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001639 -name: ProteomeDiscoverer:Xtract:Required Fitting Accuracy -def: "Accuracy required for a pattern fit to be considered valid." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001640 -name: ProteomeDiscoverer:Xtract:Resolution At 400 -def: "Resolution at mass 400." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001641 -name: ProteomeDiscoverer:Lowest Charge State -def: "Minimum charge state below which peptides are filtered out." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001642 -name: ProteomeDiscoverer:Highest Charge State -def: "Maximum charge above which peptides are filtered out." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001643 -name: ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores -def: "Determines whether spectra with scores above the threshold score are retained rather than filtered out." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001644 -name: ProteomeDiscoverer:Dynamic Modification -def: "Determine dynamic post-translational modifications (PTMs)." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001645 -name: ProteomeDiscoverer:Static Modification -def: "Static Modification to all occurrences of a named amino acid." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001646 -name: ProteomeDiscoverer:Mascot:Decoy Search -def: "OBSOLETE Determines whether the Proteome Discoverer application searches an additional decoy database." [PSI:MS] -comment: This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead. -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001647 -name: ProteomeDiscoverer:Mascot:Error tolerant Search -def: "Determines whether to search error-tolerant." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001648 -name: ProteomeDiscoverer:Mascot:Max MGF File Size -def: "Maximum size of the .mgf (Mascot Generic Format) file in MByte." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001649 -name: ProteomeDiscoverer:Mascot:Mascot Server URL -def: "URL (Uniform resource Locator) of the Mascot server." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001650 -name: ProteomeDiscoverer:Mascot:Number of attempts to submit the search -def: "Number of attempts to submit the Mascot search." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001651 -name: ProteomeDiscoverer:Mascot:X Static Modification -def: "Number of attempts to submit the Mascot search." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001652 -name: ProteomeDiscoverer:Mascot:User Name -def: "OBSOLETE Name of the user submitting the Mascot search." [PSI:MS] -comment: This term was made obsolete because it's recommended to use researcher (MS:1001271) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001653 -name: ProteomeDiscoverer:Mascot:Time interval between attempts to submit a search -def: "Time interval between attempts to submit a search in seconds." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001654 -name: ProteomeDiscoverer:Enzyme Name -def: "OBSOLETE Specifies the enzyme reagent used for protein digestion." [PSI:MS] -comment: This term was made obsolete because it's recommended to use cleavage agent name (MS:1001045) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001655 -name: ProteomeDiscoverer:Fragment Mass Tolerance -def: "OBSOLETE Mass tolerance used for matching fragment peaks in Da or mmu." [PSI:MS] -comment: This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead. -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001656 -name: Mascot:Instrument -def: "Type of instrument used to acquire the data in the raw file." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001657 -name: ProteomeDiscoverer:Maximum Missed Cleavage Sites -def: "Maximum number of missed cleavage sites to consider during the digest." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001658 -name: ProteomeDiscoverer:Mascot:Peptide CutOff Score -def: "Minimum score in the IonScore column that each peptide must exceed in order to be reported." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001659 -name: ProteomeDiscoverer:Precursor Mass Tolerance -def: "OBSOLETE Mass window for which precursor ions are considered to be the same species." [PSI:MS] -comment: This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead. -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001660 -name: ProteomeDiscoverer:Mascot:Protein CutOff Score -def: "Minimum protein score in the IonScore column that each protein must exceed in order to be reported." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001661 -name: ProteomeDiscoverer:Protein Database -def: "OBSOLETE Database to use in the search (configured on the Mascot server)." [PSI:MS] -comment: This term was made obsolete because it's recommended to use database name (MS:1001013) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001662 -name: ProteomeDiscoverer:Mascot:Protein Relevance Factor -def: "Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001663 -name: ProteomeDiscoverer:Target FDR Relaxed -def: "Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001664 -name: ProteomeDiscoverer:Target FDR Strict -def: "Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001665 -name: ProteomeDiscoverer:Mascot:Taxonomy -def: "OBSOLETE Limits searches to entries from a particular species or group of species." [PSI:MS] -comment: This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001666 -name: ProteomeDiscoverer:Use Average Precursor Mass -def: "OBSOLETE Use average mass for the precursor." [PSI:MS] -comment: This term was made obsolete because it's recommended to use parent mass type average (MS:1001212) instead. -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001667 -name: Mascot:use MudPIT scoring -def: "OBSOLETE Determines whether to use MudPIT or normal scoring." [PSI:MS] -comment: This term was made obsolete because it's recommended to use Mascot:ProteinScoringMethod (MS:1001318) instead. -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -is_obsolete: true -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001668 -name: ProteomeDiscoverer:Absolute XCorr Threshold -def: "Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001669 -name: ProteomeDiscoverer:SEQUEST:Calculate Probability Score -def: "Determines whether to calculate a probability score for every peptide match." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001670 -name: ProteomeDiscoverer:SEQUEST:CTerminal Modification -def: "Dynamic C-terminal modification that is used during the search." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001671 -name: ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage -def: "Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001672 -name: ProteomeDiscoverer:SEQUEST:Max Identical Modifications Per Peptide -def: "Maximum number of identical modifications that a single peptide can have." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001673 -name: ProteomeDiscoverer:Max Modifications Per Peptide -def: "Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001674 -name: ProteomeDiscoverer:SEQUEST:Maximum Peptides Considered -def: "Maximum number of peptides that are searched and scored per spectrum." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001675 -name: ProteomeDiscoverer:Maximum Peptides Output -def: "Maximum number of peptide matches reported per spectrum." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001676 -name: ProteomeDiscoverer:Maximum Protein References Per Peptide -def: "Maximum number of proteins that a single identified peptide can be associated with during protein assembly." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001677 -name: ProteomeDiscoverer:SEQUEST:NTerminal Modification -def: "Dynamic N-terminal modification that is used during the search." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001678 -name: ProteomeDiscoverer:Peptide CTerminus -def: "Static modification for the C terminal of the peptide used during the search." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001679 -name: ProteomeDiscoverer:Peptide NTerminus -def: "Static modification for the N terminal of the peptide used during the search." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001680 -name: ProteomeDiscoverer:SEQUEST:Peptide Relevance Factor -def: "Specifies a factor to apply to the protein score." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001681 -name: ProteomeDiscoverer:Protein Relevance Threshold -def: "Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001682 -name: ProteomeDiscoverer:Search Against Decoy Database -def: "OBSOLETE Determines whether the Proteome Discoverer application searches against a decoy database." [PSI:MS] -comment: This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead. -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001683 -name: ProteomeDiscoverer:SEQUEST:Use Average Fragment Masses -def: "Use average masses for the fragments." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001684 -name: ProteomeDiscoverer:Use Neutral Loss a Ions -def: "Determines whether a ions with neutral loss are used for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001685 -name: ProteomeDiscoverer:Use Neutral Loss b Ions -def: "Determines whether b ions with neutral loss are used for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001686 -name: ProteomeDiscoverer:Use Neutral Loss y Ions -def: "Determines whether y ions with neutral loss are used for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001687 -name: ProteomeDiscoverer:Use Neutral Loss z Ions -def: "Determines whether z ions with neutral loss are used for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001688 -name: ProteomeDiscoverer:SEQUEST:Weight of a Ions -def: "Uses a ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001689 -name: ProteomeDiscoverer:SEQUEST:Weight of b Ions -def: "Uses b ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001690 -name: ProteomeDiscoverer:SEQUEST:Weight of c Ions -def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001691 -name: ProteomeDiscoverer:SEQUEST:Weight of d Ions -def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001692 -name: ProteomeDiscoverer:SEQUEST:Weight of v Ions -def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001693 -name: ProteomeDiscoverer:SEQUEST:Weight of w Ions -def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001694 -name: ProteomeDiscoverer:SEQUEST:Weight of x Ions -def: "Uses x ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001695 -name: ProteomeDiscoverer:SEQUEST:Weight of y Ions -def: "Uses y ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001696 -name: ProteomeDiscoverer:SEQUEST:Weight of z Ions -def: "Uses z ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001697 -name: ProteomeDiscoverer:ZCore:Protein Score Cutoff -def: "Sets a minimum protein score that each protein must exceed in order to be reported." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001698 -name: ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method -def: "Specifies which peak to select if more than one peak is found inside the integration window." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001699 -name: ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance -def: "Specifies the mass-to-charge window that enables one to look for the reporter peaks." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001700 -name: ProteomeDiscoverer:Reporter Ions Quantizer:Quantitation Method -def: "Quantitation method for isobarically labeled quantitation." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001701 -name: ProteomeDiscoverer:Spectrum Exporter:Export Format -def: "OBSOLETE Format of the exported spectra (dta, mgf or mzData)." [PSI:MS] -comment: This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001702 -name: ProteomeDiscoverer:Spectrum Exporter:File name -def: "Name of the output file that contains the exported data." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001703 -name: ProteomeDiscoverer:Search Modifications Only For Identified Proteins -def: "Influences the modifications search." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001704 -name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge1 -def: "Standard high confidence XCorr parameter for charge = 1." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001705 -name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge2 -def: "Standard high confidence XCorr parameter for charge = 2." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001706 -name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge3 -def: "Standard high confidence XCorr parameter for charge = 3." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001707 -name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge4 -def: "Standard high confidence XCorr parameter for charge >= 4." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001708 -name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge1 -def: "Standard medium confidence XCorr parameter for charge = 1." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001709 -name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge2 -def: "Standard medium confidence XCorr parameter for charge = 2." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001710 -name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge3 -def: "Standard medium confidence XCorr parameter for charge = 3." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001711 -name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge4 -def: "Standard medium confidence XCorr parameter for charge >= 4." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001712 -name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1 -def: "FT high confidence XCorr parameter for charge = 1." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001713 -name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2 -def: "FT high confidence XCorr parameter for charge = 2." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001714 -name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3 -def: "FT high confidence XCorr parameter for charge = 3." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001715 -name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4 -def: "FT high confidence XCorr parameter for charge >= 4." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001716 -name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1 -def: "FT medium confidence XCorr parameter for charge = 1." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001717 -name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2 -def: "FT medium confidence XCorr parameter for charge = 2." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001718 -name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3 -def: "FT medium confidence XCorr parameter for charge = 3." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001719 -name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4 -def: "FT medium confidence XCorr parameter for charge >= 4." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001720 -name: ProteomeDiscoverer:1. Dynamic Modification -def: "OBSOLETE ProteomeDiscoverer's 1st dynamic post-translational modification (PTM) input parameter." [PSI:PI] -comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001721 -name: ProteomeDiscoverer:2. Dynamic Modification -def: "OBSOLETE ProteomeDiscoverer's 2nd dynamic post-translational modification (PTM) input parameter." [PSI:PI] -comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001722 -name: ProteomeDiscoverer:3. Dynamic Modification -def: "OBSOLETE ProteomeDiscoverer's 3rd dynamic post-translational modification (PTM) input parameter." [PSI:PI] -comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001723 -name: ProteomeDiscoverer:4. Dynamic Modification -def: "OBSOLETE ProteomeDiscoverer's 4th dynamic post-translational modification (PTM) input parameter." [PSI:PI] -comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001724 -name: ProteomeDiscoverer:Static Modification for X -def: "Static Modification for X." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001725 -name: ProteomeDiscoverer:Initial minimal peptide probability -def: "Minimal initial peptide probability to contribute to analysis." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001726 -name: ProteomeDiscoverer:Minimal peptide probability -def: "Minimum adjusted peptide probability contributing to protein probability." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001727 -name: ProteomeDiscoverer:Minimal peptide weight -def: "Minimum peptide weight contributing to protein probability." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001728 -name: ProteomeDiscoverer:Number of input1 spectra -def: "Number of spectra from 1+ precursor ions." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001729 -name: ProteomeDiscoverer:Number of input2 spectra -def: "Number of spectra from 2+ precursor ions." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001730 -name: ProteomeDiscoverer:Number of input3 spectra -def: "Number of spectra from 3+ precursor ions." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001731 -name: ProteomeDiscoverer:Number of input4 spectra -def: "Number of spectra from 4+ precursor ions." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001732 -name: ProteomeDiscoverer:Number of input5 spectra -def: "Number of spectra from 5+ precursor ions." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001733 -name: ProteomeDiscoverer:Number of predicted correct proteins -def: "Total number of predicted correct protein ids (sum of probabilities)." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001734 -name: ProteomeDiscoverer:Organism -def: "OBSOLETE Sample organism (used for annotation purposes)." [PSI:MS] -comment: This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001735 -name: ProteomeDiscoverer:Reference Database -def: "OBSOLETE Full path database name." [PSI:MS] -comment: This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001736 -name: ProteomeDiscoverer:Residue substitution list -def: "Residues considered equivalent when comparing peptides." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001737 -name: ProteomeDiscoverer:Source file extension -def: "OBSOLETE File type (if not pepXML)." [PSI:MS] -comment: This term was made obsolete because it's recommended to use mass spectrometer file format (MS:1000560) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001738 -name: ProteomeDiscoverer:Source Files -def: "OBSOLETE Input pepXML files." [PSI:MS] -comment: This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001739 -name: ProteomeDiscoverer:Source Files old -def: "OBSOLETE Input pepXML files (old)." [PSI:MS] -comment: This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001740 -name: ProteomeDiscoverer:WinCyg reference database -def: "Windows full path for database." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001741 -name: ProteomeDiscoverer:WinCyg source files -def: "Windows pepXML file names." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001742 -name: LTQ Orbitrap Velos -def: "Finnigan LTQ Orbitrap Velos MS." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1001743 -name: ProteomeDiscoverer:Mascot:Weight of A Ions -def: "Determines if to use A ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001744 -name: ProteomeDiscoverer:Mascot:Weight of B Ions -def: "Determines if to use B ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001745 -name: ProteomeDiscoverer:Mascot:Weight of C Ions -def: "Determines if to use C ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001746 -name: ProteomeDiscoverer:Mascot:Weight of D Ions -def: "Determines if to use D ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001747 -name: ProteomeDiscoverer:Mascot:Weight of V Ions -def: "Determines if to use V ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001748 -name: ProteomeDiscoverer:Mascot:Weight of W Ions -def: "Determines if to use W ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001749 -name: ProteomeDiscoverer:Mascot:Weight of X Ions -def: "Determines if to use X ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001750 -name: ProteomeDiscoverer:Mascot:Weight of Y Ions -def: "Determines if to use Y ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001751 -name: ProteomeDiscoverer:Mascot:Weight of Z Ions -def: "Determines if to use z ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001752 -name: ProteomeDiscoverer:Spectrum Selector:Use New Precursor Reevaluation -def: "Determines if to use precursor reevaluation." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001753 -name: ProteomeDiscoverer:Spectrum Selector:SN Threshold FTonly -def: "Signal-to-Noise ratio below which peaks are removed (in FT mode only)." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001754 -name: ProteomeDiscoverer:Mascot:Please Do not Touch this -def: "Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001755 -name: contact phone number -def: "Phone number of the contact person or organization." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001756 -name: contact fax number -def: "Fax number for the contact person or organization." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001757 -name: contact toll-free phone number -def: "Toll-free phone number of the contact person or organization." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000585 ! contact attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001758 -name: Mascot:SigThresholdType -def: "Significance threshold type used in Mascot reporting (either 'identity' or 'homology')." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001759 -name: Mascot:ProteinGrouping -def: "Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam's razor' or 'family clustering')." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001760 -name: Percolator:features -def: "List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002107 ! Percolator input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001761 -name: ACQUITY UPLC -def: "Waters LC-system ACQUITY UPLC." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001762 -name: ACQUITY UPLC H-Class -def: "Waters LC-system ACQUITY UPLC H-Class." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001763 -name: ACQUITY UPLC H-Class Bio -def: "Waters LC-system ACQUITY UPLC H-Class Bio." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001764 -name: ACQUITY UPLC I-Class -def: "Waters LC-system ACQUITY UPLC I-Class." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001765 -name: ACQUITY UPLC Systems with 2D Technology -def: "Waters LC-system ACQUITY UPLC Systems with 2D Technology." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001766 -name: nanoACQUITY UPLC -def: "Waters LC-system nanoACQUITY UPLC." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001767 -name: nanoACQUITY UPLC System with 1D Technology -def: "Waters LC-system nanoACQUITY UPLC System with 1D Technology." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001768 -name: nanoACQUITY UPLC with HDX Technology -def: "Waters LC-system nanoACQUITY UPLC with HDX Technology." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001769 -name: TRIZAIC UPLC nanoTile -def: "Waters LC-system TRIZAIC UPLC nanoTile." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001770 -name: GCT Premier -def: "Waters oa-ToF based GCT Premier." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001771 -name: MALDI Synapt G2 HDMS -def: "Waters oa-ToF based MALDI Synapt G2 HDMS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001772 -name: MALDI Synapt G2 MS -def: "Waters oa-ToF based MALDI Synapt G2 MS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001773 -name: MALDI Synapt G2-S HDMS -def: "Waters oa-ToF based MALDI Synapt G2 MS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001774 -name: MALDI Synapt G2-S MS -def: "Waters oa-ToF based MALDI Synapt G2-S MS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001775 -name: MALDI Synapt HDMS -def: "Waters oa-ToF based MALDI Synapt HDMS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001776 -name: MALDI Synapt MS -def: "Waters oa-ToF based MALDI Synapt MS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001777 -name: Synapt G2 HDMS -def: "Waters oa-ToF based Synapt G2 HDMS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001778 -name: Synapt G2 MS -def: "Waters oa-ToF based Synapt G2 MS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001779 -name: Synapt G2-S HDMS -def: "Waters oa-ToF based Synapt G2-S HDMS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001780 -name: Synapt G2-S MS -def: "Waters oa-ToF based Synapt G2-S MS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001781 -name: Synapt HDMS -def: "Waters oa-ToF based Synapt HDMS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001782 -name: Synapt MS -def: "Waters oa-ToF based Synapt MS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001783 -name: Xevo G2 Q-Tof -def: "Waters oa-ToF based Xevo G2 Q-Tof." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001784 -name: Xevo G2 Tof -def: "Waters oa-ToF based Xevo G2 Tof." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001785 -name: Xevo Q-Tof -def: "Waters oa-ToF based Xevo Q-Tof." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001786 -name: 3100 -def: "Waters quadrupole based 3100." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001787 -name: Acquity SQD -def: "Waters quadrupole based Acquity SQD." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001788 -name: Acquity TQD -def: "Waters quadrupole based Acquity TQD." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001789 -name: Quattro micro GC -def: "Waters (triple) quadrupole based Quattro micro GC." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001790 -name: Xevo TQ MS -def: "Waters quadrupole based Xevo TQ MS." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001791 -name: Xevo TQD -def: "Waters quadrupole based Xevo TQD." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001792 -name: Xevo TQ-S -def: "Waters quadrupole based Xevo TQ-S." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1001793 -name: Mascot:PreferredTaxonomy -def: "NCBI TaxID taxonomy ID to prefer when two or more proteins match the same set of peptides or when protein entry in database represents multiple sequences." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001795 -name: Empower -def: "Waters Empower software for liquid chromatography and mass spectrometry acquisition." [PSI:MS] -is_a: MS:1000694 ! Waters software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1001796 -name: UNIFY -def: "Waters UNIFY software for liquid chromatography and mass spectrometry acquisition." [PSI:MS] -is_a: MS:1000694 ! Waters software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1001797 -name: travelling wave ion mobility mass spectrometer -def: "OBSOLETE An ion mobility mass spectrometry technique based on the superimposition of travelling voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide." [PSI:MS] -comment: This child of the former purgatory term ion mobility spectrometry was made obsolete. -synonym: "TWIMS" EXACT [] -is_obsolete: true - -[Term] -id: MS:1001798 -name: LECO software -def: "LECO software for data acquisition and analysis." [PSI:MS] -is_a: MS:1000531 ! software - -[Term] -id: MS:1001799 -name: ChromaTOF software -def: "Software for acquisition, processing and analysis of data for LECO instruments." [PSI:MS] -is_a: MS:1001455 ! acquisition software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software -is_a: MS:1001798 ! LECO software - -[Term] -id: MS:1001800 -name: LECO instrument model -def: "LECO instrument model." [PSI:MS] -is_a: MS:1000031 ! instrument model - -[Term] -id: MS:1001801 -name: Pegasus HRT -def: "LECO high resolution time-of-flight GC mass spectrometer." [PSI:MS] -is_a: MS:1001800 ! LECO instrument model - -[Term] -id: MS:1001802 -name: Citius HRT -def: "LECO high resolution time-of-flight LC mass spectrometer." [PSI:MS] -is_a: MS:1001800 ! LECO instrument model - -[Term] -id: MS:1001803 -name: Pegasus -def: "LECO GC time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1001800 ! LECO instrument model - -[Term] -id: MS:1001804 -name: TruTOF -def: "LECO bench-top GC time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1001800 ! LECO instrument model - -[Term] -id: MS:1001805 -name: quantification datatype -def: "The data type of the value reported in a QuantLayer." [PSI:MS] -is_a: MS:1001129 ! quantification information - -[Term] -id: MS:1001806 -name: quantification object attribute -def: "Attributes describing the details of an object relevant for reporting quantification workflows or values." [PSI:MS] -is_a: MS:1001129 ! quantification information - -[Term] -id: MS:1001807 -name: study variable attribute -def: "Attribute describing a study variable." [PSI:MS] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1001808 -name: technical replicate -def: "The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001807 ! study variable attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001809 -name: biological replicate -def: "The study variable is 'biological replicate'. This means, the run was generated from another individual or sample." [PSI:MS] -is_a: MS:1001807 ! study variable attribute - -[Term] -id: MS:1001810 -name: experimental condition 'case' -def: "The experimental condition is 'case' in contrast to 'control'." [PSI:MS] -is_a: MS:1001807 ! study variable attribute - -[Term] -id: MS:1001811 -name: experimental condition 'control' -def: "The experimental condition is 'control' in contrast to 'case'." [PSI:MS] -is_a: MS:1001807 ! study variable attribute - -[Term] -id: MS:1001812 -name: experimental condition 'disease' -def: "The experimental condition is 'disease' in contrast to 'healthy'." [PSI:MS] -is_a: MS:1001807 ! study variable attribute - -[Term] -id: MS:1001813 -name: experimental condition 'healthy' -def: "The experimental condition is 'healthy' in contrast to 'disease'." [PSI:MS] -is_a: MS:1001807 ! study variable attribute - -[Term] -id: MS:1001814 -name: generic experimental condition -def: "The experimental condition is given in the value of this term." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001807 ! study variable attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001815 -name: time series, time point X -def: "The experimental design followed a time series design. The time point of this run is given in the value of this term." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1001807 ! study variable attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001816 -name: dilution series, concentration X -def: "The experimental design followed a dilution series design. The concentration of this run is given in the value of this term." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001807 ! study variable attribute -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001817 -name: raw file attribute -def: "Attribute describing a raw file." [PSI:MS] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1001818 -name: one sample run -def: "The raw file contains the run of one sample (e.g. spectral counting, LC-MS label-free)." [PSI:MS] -is_a: MS:1001817 ! raw file attribute - -[Term] -id: MS:1001819 -name: two sample run -def: "The raw file contains the run of two samples (e.g. SILAC, metabolic labelling)." [PSI:MS] -is_a: MS:1001817 ! raw file attribute - -[Term] -id: MS:1001820 -name: three sample run -def: "The raw file contains the run of three samples (e.g. 3-plex SILAC)." [PSI:MS] -is_a: MS:1001817 ! raw file attribute - -[Term] -id: MS:1001821 -name: four sample run -def: "The raw file contains the run of four samples (e.g. 4-plex iTraq)." [PSI:MS] -is_a: MS:1001817 ! raw file attribute - -[Term] -id: MS:1001822 -name: eight sample run -def: "The raw file contains the run of eight samples (e.g. 8-plex iTraq)." [PSI:MS] -is_a: MS:1001817 ! raw file attribute - -[Term] -id: MS:1001823 -name: raw files group attribute -def: "Attribute describing, how raw files build a raw file group." [PSI:MS] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1001824 -name: merge of runs of 1D gel bands -def: "Attribute describing, how raw files build a raw file group." [PSI:MS] -is_a: MS:1001823 ! raw files group attribute - -[Term] -id: MS:1001825 -name: feature list attribute -def: "Attribute describing a feature list." [PSI:MS] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1001826 -name: mass trace reporting: rectangles -def: "The mass trace of the features of this feature list specifies rectangles. Each mass trace has the syntax (RT_start,MZ_start,RT_end,MZ_end), i.e. opposite corners are given." [PSI:MS] -is_a: MS:1001825 ! feature list attribute - -[Term] -id: MS:1001827 -name: mass trace reporting: polygons -def: "The mass trace of the features of this feature list specifies polygons. Each mass trace has the syntax (RT_1, MZ_1, RT_2, MZ_2, ... , RT_i, MZ_i, ... , RT_n, MZ_n), where the line (RT_n, MZ_n)->(RT_1, MZ_1) is implicit." [PSI:MS] -is_a: MS:1001825 ! feature list attribute - -[Term] -id: MS:1001828 -name: feature attribute -def: "Attribute describing a feature." [PSI:MS] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1001829 -name: SRM transition ID -def: "Identifier for an SRM transition in an external document describing additional information about the transition." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001828 ! feature attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001830 -name: Progenesis LC-MS -def: "Software from Nonlinear Dynamics for LC-MS label-free workflow." [PSI:MS] -is_a: MS:1001139 ! quantitation software name - -[Term] -id: MS:1001831 -name: SILACAnalyzer -def: "Software for SILAC workflow." [PSI:MS] -is_a: MS:1001139 ! quantitation software name -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1001832 -name: quantitation software comment or customizations -def: "Quantitation software comment or any customizations to the default setup of the software." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001129 ! quantification information -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001833 -name: quantitation analysis summary -def: "The overall workflow of this quantitation report." [PSI:PI] -is_a: MS:1001129 ! quantification information - -[Term] -id: MS:1001834 -name: LC-MS label-free quantitation analysis -def: "LC-MS label-free workflow (RT m/z map)." [PSI:PI] -is_a: MS:1001833 ! quantitation analysis summary - -[Term] -id: MS:1001835 -name: SILAC quantitation analysis -def: "SILAC workflow (heavy, light, and sometimes medium peak)." [PSI:PI] -is_a: MS:1001833 ! quantitation analysis summary - -[Term] -id: MS:1001836 -name: spectral counting quantitation analysis -def: "Spectral counting workflow (number of identified MS2 spectra as approximation of peptide / protein quant)." [PSI:PI] -is_a: MS:1001833 ! quantitation analysis summary - -[Term] -id: MS:1001837 -name: iTRAQ quantitation analysis -def: "Quantification analysis using the SCIEX amine-reactive isobaric tags for relative and absolute quantification (iTRAQ) labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in the 114-121 m/z range." [PSI:PI, PMID:15385600] -is_a: MS:1002009 ! isobaric label quantitation analysis - -[Term] -id: MS:1001838 -name: SRM quantitation analysis -def: "Selected Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair)." [PSI:PI] -is_a: MS:1001833 ! quantitation analysis summary - -[Term] -id: MS:1001839 -name: metabolic labeling 14N / 15N quantitation analysis -def: "Metabolic labeling workflow (heavy and light versions of peptides, depending on number of nitrogens)." [PSI:PI] -is_a: MS:1001833 ! quantitation analysis summary - -[Term] -id: MS:1001840 -name: LC-MS feature intensity -def: "Maximum peak intensity of the LC-MS feature." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001841 -name: LC-MS feature volume -def: "Real (intensity times area) volume of the LC-MS feature." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001842 -name: sequence-level spectral count -def: "The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001843 -name: MS1 feature maximum intensity -def: "Maximum intensity of MS1 feature." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001844 -name: MS1 feature area -def: "Area of MS1 feature." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001845 -name: peak area -def: "OBSOLETE Area of MS1 peak (e.g. SILAC, 15N)." [PSI:PI] -comment: This term was made obsolete because it was a duplication of MS:1001844. -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001846 -name: isotopic pattern area -def: "Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001847 -name: reporter ion intensity -def: "Intensity of MS2 reporter ion (e.g. iTraq)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001848 -name: simple ratio of two values -def: "Simple ratio of two values (enumerator and denominator)." [PSI:PI] -is_a: MS:1002066 ! ratio calculation method - -[Term] -id: MS:1001849 -name: sum of MatchedFeature values -def: "OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values." [PSI:PI] -comment: This term was made obsolete because the concept MatchedFeature was dropped. -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002735 ! feature-level quantification datatype -is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001850 -name: normalized peptide value -def: "Normalized peptide value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001851 -name: protein value: sum of peptide values -def: "Protein quantification value calculated as sum of peptide values." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001852 -name: normalized protein value -def: "Normalized protein value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001853 -name: max fold change -def: "Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001854 -name: ANOVA p-value -def: "Global datatype: p-value of ANOVA of group means (e.g. Progenesis)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002072 ! p-value -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001855 -name: t-test p-value -def: "P-value of t-Test of two groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002072 ! p-value -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001856 -name: reporter ion raw value -def: "Intensity (or area) of MS2 reporter ion (e.g. iTraq)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001857 -name: reporter ion normalized value -def: "Normalized value of MS2 reporter ion (e.g. iTraq)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001858 -name: XIC area -def: "Area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001859 -name: normalized XIC area -def: "Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001860 -name: protein value: mean of peptide ratios -def: "Protein quantification value calculated as mean of peptide ratios." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001861 -name: quantification data processing -def: "Terms used to describe types of quantification data processing." [PSI:MS] -relationship: part_of MS:1001000 ! spectrum interpretation - -[Term] -id: MS:1001862 -name: normalization to mean of sum of all proteins -def: "Normalization of protein values to the mean of the sum of all protein PSM counts (e.g. spectral counting)." [PSI:MS] -is_a: MS:1001861 ! quantification data processing - -[Term] -id: MS:1001863 -name: quantile normalization, proteins -def: "Normalization of protein values to approach the same distribution." [PSI:MS] -is_a: MS:1001861 ! quantification data processing - -[Term] -id: MS:1001864 -name: quantile normalization, peptides -def: "Normalization of peptide values to approach the same distribution." [PSI:MS] -is_a: MS:1001861 ! quantification data processing - -[Term] -id: MS:1001865 -name: Progenesis automatic alignment -def: "Automatic RT alignment of Progenesis software." [PSI:MS] -is_a: MS:1001861 ! quantification data processing - -[Term] -id: MS:1001866 -name: Progenesis manual alignment -def: "RT alignment of Progenesis software using automatic and manual vectors." [PSI:MS] -is_a: MS:1001861 ! quantification data processing - -[Term] -id: MS:1001867 -name: Progenesis normalization -def: "Normalization as performed by Progenesis LC-MS." [PSI:MS] -is_a: MS:1001861 ! quantification data processing - -[Term] -id: MS:1001868 -name: distinct peptide-level q-value -def: "Estimation of the q-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs, possibly with different mass modifications, mapping to the same sequence have been collapsed to one entry)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002484 ! peptide-level statistical threshold -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001869 -name: protein-level q-value -def: "Estimation of the q-value for proteins." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001116 ! single protein identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001870 -name: peptide sequence-level p-value -def: "Estimation of the p-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001092 ! peptide sequence-level identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001871 -name: protein-level p-value -def: "Estimation of the p-value for proteins." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001116 ! single protein identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001872 -name: peptide sequence-level e-value -def: "Estimation of the e-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001092 ! peptide sequence-level identification statistic -relationship: has_domain MS:1002306 ! value greater than zero -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001873 -name: protein-level e-value -def: "Estimation of the e-value for proteins." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001116 ! single protein identification statistic -relationship: has_domain MS:1002306 ! value greater than zero -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001874 -name: FDRScore -def: "OBSOLETE A smoothing of the distribution of q-values calculated for PSMs from individual search engines, such that ordering of result quality is maintained and all FDRScore values are guaranteed to have a value > 0." [PMID:19253293] -comment: This term was made obsolete because it was split into the more specific terms for PSM-level FDRScore (1002355), distinct peptide-level FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein group-level FDRScore (MS:1002374). -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1001153 ! search engine specific score -is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001875 -name: modification motif -def: "The regular expression describing the sequence motif for a modification." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001056 ! modification specificity rule -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001876 -name: modification probability -def: "The a priori probability of a modification." [PSI:PI] -is_a: MS:1001056 ! modification specificity rule - -[Term] -id: MS:1001877 -name: ChromaTOF HRT software -def: "Software for acquisition, processing and analysis of data for LECO instruments." [PSI:MS] -is_a: MS:1001455 ! acquisition software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software -is_a: MS:1001798 ! LECO software - -[Term] -id: MS:1001878 -name: MALDI Solutions Microbial Identification -def: "Shimadzu Biotech software for data acquisition, processing, and analysis." [PSI:MS] -is_a: MS:1001558 ! MALDI Solutions - -[Term] -id: MS:1001879 -name: offset voltage -def: "The potential difference between two adjacent interface voltages affecting in-source collision induced dissociation." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000482 ! source attribute -relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001880 -name: in-source collision-induced dissociation -def: "The dissociation of an ion as a result of collisional excitation during ion transfer from an atmospheric pressure ion source and the mass spectrometer vacuum." [PSI:MS] -is_a: MS:1000044 ! dissociation method - -[Term] -id: MS:1001881 -name: mz5 format -def: "mz5 file format, modelled after mzML." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1001882 -name: transition validation attribute -def: "Attributes of the quality of a transition that affect its selection as appropriate." [PSI:MS] -relationship: part_of MS:1000908 ! transition - -[Term] -id: MS:1001883 -name: coefficient of variation -def: "Variation of a set of signal measurements calculated as the standard deviation relative to the mean." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1001882 ! transition validation attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001884 -name: signal-to-noise ratio -def: "Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1001882 ! transition validation attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001885 -name: command-line parameters -def: "Parameters string passed to a command-line interface software application, omitting the executable name." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000630 ! data processing parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001886 -name: SQID -def: "Software for data analysis of peptides and proteins." [PSI:MS] -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1001887 -name: SQID:score -def: "The SQID result 'Score'." [PSI:PI] -is_a: MS:1001143 ! PSM-level search engine specific statistic - -[Term] -id: MS:1001888 -name: SQID:deltaScore -def: "The SQID result 'deltaScore'." [PSI:PI] -is_a: MS:1001143 ! PSM-level search engine specific statistic - -[Term] -id: MS:1001889 -name: SQID:protein score -def: "The SQID result 'protein score'." [PSI:PI] -is_a: MS:1002363 ! search engine specific score for proteins - -[Term] -id: MS:1001890 -name: Progenesis:protein normalised abundance -def: "The data type normalised abundance for proteins produced by Progenesis LC-MS." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001891 -name: Progenesis:peptide normalised abundance -def: "The data type normalised abundance for peptides produced by Progenesis LC-MS." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001892 -name: Progenesis:protein raw abundance -def: "The data type raw abundance for proteins produced by Progenesis LC-MS." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001893 -name: Progenesis:peptide raw abundance -def: "The data type raw abundance for peptide produced by Progenesis LC-MS." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001894 -name: Progenesis:confidence score -def: "The data type confidence score produced by Progenesis LC-MS." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001895 -name: Progenesis:peptide count -def: "The data type peptide count produced by Progenesis LC-MS." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001896 -name: Progenesis:feature intensity -def: "The data type feature intensity produced by Progenesis LC-MS." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001897 -name: MaxQuant:peptide counts (unique) -def: "The data type peptide counts (unique) produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001898 -name: MaxQuant:peptide counts (all) -def: "The data type peptide counts (all) produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001899 -name: MaxQuant:peptide counts (razor+unique) -def: "The data type peptide counts (razor+unique) produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001900 -name: MaxQuant:sequence length -def: "The data type sequence length produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001901 -name: MaxQuant:PEP -def: "The data type PEP (posterior error probability) produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001902 -name: MaxQuant:LFQ intensity -def: "The data type LFQ intensity produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001903 -name: MaxQuant:feature intensity -def: "The data type feature intensity produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001904 -name: MaxQuant:MS/MS count -def: "The data type MS2 count produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1001905 -name: emPAI value -def: "The emPAI value of protein abundance, produced from the emPAI algorithm." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001906 -name: APEX value -def: "The APEX value of protein abundance, produced from the APEX software." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001907 -name: retention time window width -def: "The full width of a retention time window for a chromatographic peak." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000915 ! retention time window attribute -relationship: has_units UO:0000010 ! second -relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001908 -name: ISQ -def: "Thermo Scientific ISQ single quadrupole MS with the ExtractraBrite source." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1001909 -name: Velos Plus -def: "Thermo Scientific second generation Velos." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1001910 -name: LTQ Orbitrap Elite -def: "Thermo Scientific LTQ Orbitrap Elite, often just referred to as the Orbitrap Elite." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1001911 -name: Q Exactive -def: "Thermo Scientific Q Exactive." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1001912 -name: PinPoint -def: "Thermo Scientific PinPoint SRM analysis software." [PSI:MS] -is_a: MS:1000693 ! Thermo Finnigan software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1001913 -name: S-lens voltage -def: "Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000482 ! source attribute -relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001914 -name: pymzML -def: "Python module to interface mzML Data." [PSI:MS] -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1001915 -name: leukocyte elastase -def: "Enzyme leukocyte elastase (EC 3.4.21.37)." [BRENDA:3.4.21.37] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001957 ! (?<=[ALIV])(?!P) - -[Term] -id: MS:1001916 -name: proline endopeptidase -def: "Enzyme proline endopeptidase (EC 3.4.21.26)." [BRENDA:3.4.21.26] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001958 ! (?<=[HKR]P)(?!P) - -[Term] -id: MS:1001917 -name: glutamyl endopeptidase -def: "Enzyme glutamyl endopeptidase (EC 3.4.21.19)." [BRENDA:3.4.21.19] -synonym: "staphylococcal protease" EXACT [] -synonym: "Glu-C" EXACT [] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001959 ! (?<=[^E]E) - -[Term] -id: MS:1001918 -name: 2-iodobenzoate -def: "Chemical iodobenzoate. Cleaves after W." [PubChem_Compound:4739928] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001960 ! (?<=W) - -[Term] -id: MS:1001919 -name: ProteomeXchange accession number -def: "Main identifier of a ProteomeXchange dataset." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001921 -name: ProteomeXchange accession number version number -def: "Version number of a ProteomeXchange accession number." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001922 -name: Digital Object Identifier (DOI) -def: "DOI unique identifier of a publication." [PSI:PI, http://dx.doi.org] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -synonym: "doi" EXACT [] -is_a: MS:1000878 ! external reference identifier -relationship: has_regexp MS:1002480 ! (10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+) -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001923 -name: external reference keyword -def: "Free text attribute that can enrich the information about an entity." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002840 ! external reference data -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001924 -name: journal article keyword -def: "Keyword present in a scientific publication." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001923 ! external reference keyword -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001925 -name: submitter keyword -def: "Keyword assigned by the data submitter." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001923 ! external reference keyword -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001926 -name: curator keyword -def: "Keyword assigned by a data curator." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001923 ! external reference keyword -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001927 -name: Tranche file hash -def: "Hash assigned by the Tranche resource to an individual file." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001928 -name: Tranche project hash -def: "Hash assigned by the Tranche resource to a whole project." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001929 -name: PRIDE experiment URI -def: "URI that allows the access to one experiment in the PRIDE database." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term - -[Term] -id: MS:1001930 -name: PRIDE project URI -def: "URI that allows the access to one project in the PRIDE database." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term - -[Term] -id: MS:1001931 -name: source interface -def: "The source interface." [PSI:MS] -relationship: part_of MS:1000458 ! source - -[Term] -id: MS:1001932 -name: source interface model -def: "The source interface model." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: part_of MS:1001931 ! source interface -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001933 -name: source sprayer -def: "The source sprayer." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: part_of MS:1000458 ! source -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001934 -name: source sprayer type -def: "The source sprayer type." [PSI:MS] -relationship: part_of MS:1001933 ! source sprayer - -[Term] -id: MS:1001935 -name: source sprayer manufacturer -def: "The source sprayer manufacturer." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: part_of MS:1001933 ! source sprayer -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001936 -name: source sprayer model -def: "The source sprayer model." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: part_of MS:1001933 ! source sprayer -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001937 -name: sample plate -def: "Plate where the sample solution is spotted in a MALDI or similar instrument." [PSI:MS] -relationship: part_of MS:1000458 ! source - -[Term] -id: MS:1001938 -name: sample plate type -def: "The sample plate type." [PSI:MS] -relationship: part_of MS:1001937 ! sample plate - -[Term] -id: MS:1001939 -name: stainless steel plate -def: "Stainless steel plate." [PSI:MS] -is_a: MS:1001938 ! sample plate type - -[Term] -id: MS:1001940 -name: coated glass plate -def: "Coated glass plate." [PSI:MS] -is_a: MS:1001938 ! sample plate type - -[Term] -id: MS:1001941 -name: electrospray supply type -def: "Whether the sprayer is fed or is loaded with sample once." [PSI:MS] -relationship: part_of MS:1000458 ! source - -[Term] -id: MS:1001942 -name: static supply electrospray -def: "The sprayer is loaded with sample once." [PSI:MS] -is_a: MS:1001941 ! electrospray supply type - -[Term] -id: MS:1001943 -name: fed supply electrospray -def: "The sprayer is continuously fed with sample." [PSI:MS] -is_a: MS:1001941 ! electrospray supply type - -[Term] -id: MS:1001944 -name: Collision cell exit potential -def: "Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000510 ! precursor activation attribute -relationship: has_units UO:0000218 ! volt -synonym: "CXP" EXACT [] -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001945 -name: Pegasus 4D -def: "LECO nominal mass resolution time-of-flight GCxGC mass spectrometer." [PSI:MS] -is_a: MS:1001800 ! LECO instrument model - -[Term] -id: MS:1001946 -name: PEAKS Studio -def: "PEAKS Studio software for data analysis." [PSI:MS] -is_a: MS:1001139 ! quantitation software name -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1001947 -name: PEAKS Online -def: "PEAKS Online software for high throughput data analysis." [PSI:MS] -is_a: MS:1001139 ! quantitation software name -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1001948 -name: PEAKS Node -def: "PEAKS Node software for high throughput data analysis." [PSI:MS] -is_a: MS:1001139 ! quantitation software name -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1001949 -name: BSI software -def: "Bioinformatics Solutions Inc. Software for data processing and analysis." [PSI:MS] -is_a: MS:1000531 ! software - -[Term] -id: MS:1001950 -name: PEAKS:peptideScore -def: "The PEAKS peptide '-10lgP Score'." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001951 -name: PEAKS:proteinScore -def: "The PEAKS protein '-10lgP Score'." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001952 -name: ZCore:probScore -def: "The ZCore probability score." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001953 -name: source interface manufacturer -def: "The source interface manufacturer." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: part_of MS:1001931 ! source interface -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001954 -name: acquisition parameter -def: "Parameters used in the mass spectrometry acquisition." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: part_of MS:1001458 ! spectrum generation information -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001955 -name: no cleavage -def: "No cleavage." [PSI:MS] -is_a: MS:1001045 ! cleavage agent name - -[Term] -id: MS:1001956 -name: unspecific cleavage -def: "Unspecific cleavage." [PSI:MS] -is_a: MS:1001045 ! cleavage agent name - -[Term] -id: MS:1001957 -name: (?<=[ALIV])(?!P) -def: "Regular expression for leukocyte elastase." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001958 -name: (?<=[HKR]P)(?!P) -def: "Regular expression for proline endopeptidase." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001959 -name: (?<=[^E]E) -def: "Regular expression for glutamyl endopeptidase." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001960 -name: (?<=W) -def: "Regular expression for 2-iodobenzoate." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1001961 -name: peptide spectrum match scoring algorithm -def: "Algorithm used to score the match between a spectrum and a peptide ion." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: part_of MS:1001458 ! spectrum generation information -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001962 -name: Mascot:C13 counts -def: "C13 peaks to use in peak detection." [PSI:MS] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1001963 -name: ProteinExtractor:Weighting -def: "Weighting factor for protein list compilation by ProteinExtractor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002098 ! ProteinExtractor input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001964 -name: ProteinScape:second round Mascot -def: "Flag indicating a second round search with Mascot." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002100 ! ProteinScape input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001965 -name: ProteinScape:second round Phenyx -def: "Flag indicating a second round search with Phenyx." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002100 ! ProteinScape input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1001966 -name: product ion mobility -def: "The mobility of an MS2 product ion, as measured by ion mobility mass spectrometry." [PSI:MS] -is_a: MS:1001221 ! product ion attribute - -[Term] -id: MS:1001967 -name: product ion drift time -def: "OBSOLETE The ion drift time of an MS2 product ion." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002222 ! SRM transition attribute -relationship: has_units UO:0000028 ! millisecond -comment: This term was made obsolete because it was replaced by ion mobility drift time (MS:1002476). -is_obsolete: true -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1001968 -name: PTM localization PSM-level statistic -def: "Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence at the PSM-level." [PSI:MS] -is_a: MS:1002689 ! PTM localization single result statistic - -[Term] -id: MS:1001969 -name: phosphoRS score -def: "phosphoRS score for PTM site location at the PSM-level." [DOI:10.1021/pr200611n, PMID:22073976] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001970 -name: phosphoRS sequence probability -def: "Probability that the respective isoform is correct." [DOI:10.1021/pr200611n, PMID:22073976] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001971 -name: phosphoRS site probability -def: "Estimate of the probability that the respective site is truly phosphorylated." [DOI:10.1021/pr200611n, PMID:22073976] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001972 -name: PTM scoring algorithm version -def: "Version of the post-translational modification scoring algorithm." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001471 ! peptide modification details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001973 -name: DeBunker -def: "DeBunker software." [PSI:MS] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001974 -name: DeBunker:score -def: "Score specific to DeBunker." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001975 -name: delta m/z -def: "The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value." [PSI:MS] -synonym: "m/z difference" EXACT [] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001405 ! spectrum identification result details -relationship: has_units UO:0000166 ! parts per notation unit -relationship: has_units UO:0000187 ! percent -relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001976 -name: delta M -def: "The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value." [PSI:MS] -synonym: "mass difference" EXACT [] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001405 ! spectrum identification result details -relationship: has_units UO:0000166 ! parts per notation unit -relationship: has_units UO:0000187 ! percent -relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1001977 -name: MSQuant -def: "MSQuant software." [PSI:MS] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001978 -name: MSQuant:PTM-score -def: "The PTM score from MSQuant software." [DOI:10.1021/pr900721e, PMID:19888749] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001979 -name: MaxQuant:PTM Score -def: "The PTM score from MaxQuant software." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001980 -name: MaxQuant:Phospho (STY) Probabilities -def: "The Phospho (STY) Probabilities from MaxQuant software." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001981 -name: MaxQuant:Phospho (STY) Score Diffs -def: "The Phospho (STY) Score Diffs from MaxQuant software." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001982 -name: MaxQuant:P-site localization probability -def: "The P-site localization probability value from MaxQuant software." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001983 -name: MaxQuant:PTM Delta Score -def: "The PTM Delta Score value from MaxQuant software (Difference between highest scoring site and second highest)." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001984 -name: Ascore software -def: "Ascore software." [PSI:MS] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1001985 -name: Ascore -def: "A-score for PTM site location at the PSM-level." [DOI:10.1038/nbt1240, PMID:16964243] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001986 -name: H-Score -def: "H-Score for peptide phosphorylation site location." [DOI:10.1021/pr1006813, PMID:20836569] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1001987 -name: vacuum drying MALDI sample preparation -def: "Vacuum-drying MALDI sample preparation crystallization method." [PSI:MS] -is_a: MS:1000833 ! matrix application type - -[Term] -id: MS:1001988 -name: crushed crystal MALDI sample preparation -def: "Crushed-crystal MALDI sample preparation method." [PSI:MS] -is_a: MS:1000833 ! matrix application type - -[Term] -id: MS:1001989 -name: fast evaporation MALDI sample preparation -def: "Fast-evaporation MALDI sample preparation method." [DOI:10.1021/ac00091a044] -is_a: MS:1000833 ! matrix application type - -[Term] -id: MS:1001990 -name: overlayer MALDI sample preparation -def: "Overlayer method combining features of the crushed-crystal method and the fast-evaporation method." [PSI:MS] -is_a: MS:1000833 ! matrix application type - -[Term] -id: MS:1001991 -name: sandwich MALDI sample preparation -def: "Sandwich MALDI sample preparation method." [DOI:10.1002/(SICI)1096-9888(199706)32:6<593::AID-JMS511>3.3.CO;2-4] -is_a: MS:1000833 ! matrix application type - -[Term] -id: MS:1001992 -name: spin coating MALDI sample preparation -def: "Spin coating MALDI sample preparation method." [DOI:10.1021/cc0500710, PMID:16283807] -is_a: MS:1000833 ! matrix application type - -[Term] -id: MS:1001993 -name: quick and dirty MALDI sample preparation -def: "Quick & dirty (Q&D) sample preparation separating matrix handling from sample handling." [PSI:MS] -is_a: MS:1000833 ! matrix application type - -[Term] -id: MS:1001994 -name: top hat baseline reduction -def: "Top-hat morphological filter based on the basic morphological operations 'erosion' and 'dilatation'." [PSI:MS] -is_a: MS:1000593 ! baseline reduction - -[Term] -id: MS:1001995 -name: convex hull baseline reduction -def: "Constructs the baseline by fitting multiple parabolas to the spectrum starting with the large scale structures." [PSI:MS] -is_a: MS:1000593 ! baseline reduction - -[Term] -id: MS:1001996 -name: median baseline reduction -def: "The spectrum that will be baseline subtracted is divided into a number of segments." [PSI:MS] -is_a: MS:1000593 ! baseline reduction - -[Term] -id: MS:1001997 -name: wavelet transformation smoothing -def: "The random noise is removed by using the undecimated wavelet transform." [DOI:10.1093/bioinformatics/btl355, PMID:16820428] -is_a: MS:1000592 ! smoothing - -[Term] -id: MS:1001998 -name: sophisticated numerical annotation procedure -def: "It searches for known patterns in the measured spectrum." [DOI:10.1021/ac951158i, PMID:21619291] -synonym: "SNAP" EXACT [] -is_a: MS:1000801 ! area peak picking - -[Term] -id: MS:1001999 -name: area normalization -def: "Normalization of areas below the curves." [PSI:MS] -is_a: MS:1001484 ! intensity normalization - -[Term] -id: MS:1002000 -name: LIFT -def: "A Bruker's proprietary technique where molecular ions are initially accelerated at lower energy, then collide with inert gas in a collision cell that is then 'lifted' to high potential. The use of inert gas is optional, as it could lift also fragments provided by LID." [DOI:10.1007/s00216-003-2057-0 , PMID:12830354] -is_a: MS:1000044 ! dissociation method - -[Term] -id: MS:1002001 -name: MS1 label-based raw feature quantitation -def: "MS1 label-based raw feature quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002018 ! MS1 label-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002002 -name: MS1 label-based peptide level quantitation -def: "MS1 label-based peptide level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002018 ! MS1 label-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002003 -name: MS1 label-based protein level quantitation -def: "MS1 label-based protein level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002018 ! MS1 label-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002004 -name: MS1 label-based proteingroup level quantitation -def: "MS1 label-based proteingroup level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002018 ! MS1 label-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002005 -name: iRT retention time normalization standard -def: "A de facto standard providing the retention times at which a specific set of 10 reference peptides exit the reference chromatographic column. The kit may be obtain from Biognosys." [DOI:10.1002/pmic.201100463, http://www.biognosys.ch/products/rt-kit.html] -is_a: MS:1000901 ! retention time normalization standard - -[Term] -id: MS:1002006 -name: SRM transition type -def: "The type of the transitions, e.g. target or decoy." [PSI:MS] -synonym: "MRM transition type" EXACT [] -relationship: part_of MS:1000908 ! transition - -[Term] -id: MS:1002007 -name: target SRM transition -def: "A transition used to target a specific compound that may be in the sample." [PSI:MS] -synonym: "target MRM transition" EXACT [] -is_a: MS:1002006 ! SRM transition type - -[Term] -id: MS:1002008 -name: decoy SRM transition -def: "A transition not expected to be present in the sample and used to calculate statistical confidence of target transition detections in some workflows." [PSI:MS] -synonym: "decoy MRM transition" EXACT [] -is_a: MS:1002006 ! SRM transition type - -[Term] -id: MS:1002009 -name: isobaric label quantitation analysis -def: "Quantitation analysis using an isobaric labelling workflow." [PSI:PI] -is_a: MS:1001833 ! quantitation analysis summary - -[Term] -id: MS:1002010 -name: TMT quantitation analysis -def: "Quantitation analysis using the Thermo Fisher amine-reactive tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are measured in MS2 spectra in the 126-131 m/z." [PSI:PI, PMID:12713048] -is_a: MS:1002009 ! isobaric label quantitation analysis - -[Term] -id: MS:1002011 -name: desorption electrospray ionization -def: "Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure." [DOI:10.1126/science.1104404, PMID:15486296] -synonym: "DESI" EXACT [] -is_a: MS:1000240 ! atmospheric pressure ionization - -[Term] -id: MS:1002012 -name: Mascot:PTM site assignment confidence -def: "Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score)." [http://www.matrixscience.com/help/pt_mods_help.html#SITE] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_units UO:0000187 ! percent -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002013 -name: collision energy ramp start -def: "Collision energy at the start of the collision energy ramp." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000045 ! collision energy -relationship: has_units UO:0000266 ! electronvolt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002014 -name: collision energy ramp end -def: "Collision energy at the end of the collision energy ramp." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000045 ! collision energy -relationship: has_units UO:0000266 ! electronvolt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002015 -name: spectral count peptide level quantitation -def: "Spectral count peptide level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001836 ! spectral counting quantitation analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002016 -name: spectral count protein level quantitation -def: "Spectral count protein level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001836 ! spectral counting quantitation analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002017 -name: spectral count proteingroup level quantitation -def: "Spectral count proteingroup level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001836 ! spectral counting quantitation analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002018 -name: MS1 label-based analysis -def: "MS1 label-based analysis." [PSI:PI] -is_a: MS:1001833 ! quantitation analysis summary - -[Term] -id: MS:1002019 -name: label-free raw feature quantitation -def: "Label-free raw feature quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001834 ! LC-MS label-free quantitation analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002020 -name: label-free peptide level quantitation -def: "Label-free peptide level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001834 ! LC-MS label-free quantitation analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002021 -name: label-free protein level quantitation -def: "Label-free protein level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001834 ! LC-MS label-free quantitation analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002022 -name: label-free proteingroup level quantitation -def: "Label-free proteingroup level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001834 ! LC-MS label-free quantitation analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002023 -name: MS2 tag-based analysis -def: "MS2 tag-based analysis." [PSI:PI] -is_a: MS:1001833 ! quantitation analysis summary - -[Term] -id: MS:1002024 -name: MS2 tag-based feature level quantitation -def: "MS2 tag-based feature level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002023 ! MS2 tag-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002025 -name: MS2 tag-based peptide level quantitation -def: "MS2 tag-based peptide level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002023 ! MS2 tag-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002026 -name: MS2 tag-based protein level quantitation -def: "MS2 tag-based protein level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002023 ! MS2 tag-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002027 -name: MS2 tag-based proteingroup level quantitation -def: "MS2 tag-based proteingroup level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002023 ! MS2 tag-based analysis -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002028 -name: nucleic acid base modification -def: "Nucleic acid base modification (substitution, insertion or deletion)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001471 ! peptide modification details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002029 -name: original nucleic acid sequence -def: "Specification of the original nucleic acid sequence, prior to a modification. The value slot should hold the DNA or RNA sequence." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001471 ! peptide modification details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002030 -name: modified nucleic acid sequence -def: "Specification of the modified nucleic acid sequence. The value slot should hold the DNA or RNA sequence." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001471 ! peptide modification details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002031 -name: PASSEL transition group browser URI -def: "URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term - -[Term] -id: MS:1002032 -name: PeptideAtlas dataset URI -def: "URI that allows access to a PeptideAtlas dataset." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term - -[Term] -id: MS:1002033 -name: contact role -def: "Role of the contact person." [PSI:PI] -is_a: MS:1000585 ! contact attribute - -[Term] -id: MS:1002034 -name: first author -def: "The first of a set of authors associated with a publication or release. There may be more than one first author in cases where several authors share primary attribution." [PSI:MS] -is_a: MS:1002033 ! contact role - -[Term] -id: MS:1002035 -name: senior author -def: "The last of a set of authors associated with a publication or release. There may be more than one senior author in cases where several authors share senior attribution." [PSI:MS] -is_a: MS:1002033 ! contact role - -[Term] -id: MS:1002036 -name: co-author -def: "One of a set of authors associated with a publication or release." [PSI:MS] -is_a: MS:1002033 ! contact role - -[Term] -id: MS:1002037 -name: dataset submitter -def: "A person who submits a dataset to a repository." [PSI:MS] -is_a: MS:1002033 ! contact role - -[Term] -id: MS:1002038 -name: label free sample -def: "A sample that has not been labelled or modified. This is often referred to as \"light\" to distinguish from \"heavy\"." [PSI:PI] -synonym: "light sample" EXACT [] -is_a: MS:1000548 ! sample attribute - -[Term] -id: MS:1002039 -name: inlet attribute -def: "Inlet properties that are associated with a value." [PSI:MS] -is_a: MS:1000547 ! object attribute -relationship: part_of MS:1000458 ! source - -[Term] -id: MS:1002040 -name: inlet temperature -def: "The temperature of the inlet of a mass spectrometer." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000482 ! source attribute -is_a: MS:1002039 ! inlet attribute -relationship: has_units UO:0000012 ! kelvin -relationship: has_units UO:0000027 ! degree Celsius -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002041 -name: source temperature -def: "The temperature of the source of a mass spectrometer." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000482 ! source attribute -relationship: has_units UO:0000012 ! kelvin -relationship: has_units UO:0000027 ! degree Celsius -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002042 -name: modulation time -def: "The duration of a complete cycle of modulation in a comprehensive two-dimensional separation system, equals the length of a second dimension chromatogram, i.e., the time between two successive injections into the second column." [http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000857 ! run attribute -relationship: has_units UO:0000010 ! second -relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002043 -name: ProteinProspector -def: "ProteinProspector software for data acquisition and analysis." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002044 -name: ProteinProspector:score -def: "The ProteinProspector result 'Score'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002045 -name: ProteinProspector:expectation value -def: "The ProteinProspector result 'Expectation value'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002046 -name: native source path -def: "The original source path used for directory-based sources." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001458 ! spectrum generation information -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002047 -name: MS-GF -def: "MS-GF software used to re-score the peptide-spectrum matches." [DOI:10.1074/mcp.M110.003731, PMID:20829449] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002048 -name: MS-GF+ -synonym: "MS-GFDB" EXACT [] -def: "MS-GF+ software used to analyze the spectra." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002049 -name: MS-GF:RawScore -def: "MS-GF raw score." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002050 -name: MS-GF:DeNovoScore -def: "MS-GF de novo score." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002051 -name: MS-GF:Energy -def: "MS-GF energy score." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1002052 -name: MS-GF:SpecEValue -def: "MS-GF spectral E-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002353 ! PSM-level e-value -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002053 -name: MS-GF:EValue -def: "MS-GF E-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002353 ! PSM-level e-value -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002054 -name: MS-GF:QValue -def: "MS-GF Q-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002354 ! PSM-level q-value -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002055 -name: MS-GF:PepQValue -def: "MS-GF peptide-level Q-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002056 -name: MS-GF:PEP -def: "MS-GF posterior error probability." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002057 -name: modification specificity protein N-term -def: "As parameter for search engine: apply the modification only at the N-terminus of a protein." [PSI:PI] -is_a: MS:1001056 ! modification specificity rule - -[Term] -id: MS:1002058 -name: modification specificity protein C-term -def: "As parameter for search engine: apply the modification only at the C-terminus of a protein." [PSI:PI] -is_a: MS:1001056 ! modification specificity rule - -[Term] -id: MS:1002059 -name: Microsoft Excel -def: "Microsoft Excel (can be used for spectral counting)." [PSI:PI] -is_a: MS:1001139 ! quantitation software name - -[Term] -id: MS:1002060 -name: database UniProtKB/TrEMBL -def: "The name of the UniProtKB/TrEMBL database." [PSI:PI] -is_a: MS:1002126 ! database UniProtKB - -[Term] -id: MS:1002061 -name: decoy DB from UniProtKB/TrEMBL -def: "OBSOLETE Decoy database from a TrEMBL protein sequence database." [PSI:PI] -comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. -is_obsolete: true - -[Term] -id: MS:1002062 -name: metabolic labelling: natural N (mainly 14N) -def: "Metabolic labelling: natural N (mainly 14N)." [PSI:PI] -is_a: MS:1001055 ! modification parameters - -[Term] -id: MS:1002063 -name: FindPairs -def: "Software e.g. for SILAC and 14N/15N workflow, part of the PeakQuant suite." [http://www.medizinisches-proteom-center.de/software] -is_a: MS:1001139 ! quantitation software name - -[Term] -id: MS:1002064 -name: peptide consensus RT -def: "Peptide consensus retention time." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002065 -name: peptide consensus m/z -def: "Peptide consensus mass/charge ratio." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002066 -name: ratio calculation method -def: "Method used to calculate the ratio." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002067 -name: protein value: median of peptide ratios -def: "Protein quantification value calculated as median of peptide ratios." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002068 -name: metabolic labelling: heavy N (mainly 15N) -def: "Metabolic labelling: heavy N (mainly 15N)." [PSI:PI] -is_a: MS:1001055 ! modification parameters - -[Term] -id: MS:1002069 -name: metabolic labelling purity -def: "Metabolic labelling: Description of labelling purity. Usually the purity of feeding material (e.g. 95%), or the inclusion rate derived from isotopic peak pattern shape." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001055 ! modification parameters -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002070 -name: t-test -def: "Perform a t-test (two groups). Specify in string value, whether paired / unpaired, variance equal / different, one- / two-sided version is performed." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001861 ! quantification data processing -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002071 -name: ANOVA-test -def: "Perform an ANOVA-test (more than two groups). Specify in string value, which version is performed." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001861 ! quantification data processing -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002072 -name: p-value -def: "P-value as result of one of the processing steps described. Specify in the description, which processing step it was." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002073 -name: mzIdentML format -def: "The mzIdentML format for peptide and protein identification data from the PSI. File extension '.mzid'." [PSI:PI, http://www.psidev.info/mzidentml] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1002074 -name: quantification file format -def: "File format containing quantification results." [PSI:PI] -is_a: MS:1001459 ! file format - -[Term] -id: MS:1002075 -name: mzQuantML format -def: "The mzQuantML format for quantification data from the PSI. File extension '.mzq'." [PSI:PI, http://www.psidev.info/mzquantml] -is_a: MS:1002074 ! quantification file format - -[Term] -id: MS:1002076 -name: PAnalyzer -def: "PAnalyzer software for getting protein evidence categories." [http://code.google.com/p/ehu-bio/wiki/PAnalyzer] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002077 -name: impact -def: "Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] -is_a: MS:1001536 ! Bruker Daltonics micrOTOF series - -[Term] -id: MS:1002078 -name: ProteomeDiscoverer:1. Static Modification -def: "OBSOLETE ProteomeDiscoverer's 1st static post-translational modification (PTM) input parameter." [PSI:PI] -comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002079 -name: ProteomeDiscoverer:2. Static Modification -def: "OBSOLETE ProteomeDiscoverer's 2nd static post-translational modification (PTM) input parameter." [PSI:PI] -comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002080 -name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before -def: "Precursor clipping range before." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002081 -name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After -def: "Precursor clipping range after." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002082 -name: first column elution time -def: "The time of elution from the first chromatographic column in the chromatographic separation step, relative to the start of chromatography on the first column." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000503 ! scan attribute -relationship: has_units UO:0000010 ! second -relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002083 -name: second column elution time -def: "The time of elution from the second chromatographic column in the chromatographic separation step, relative to the start of the chromatography on the second column." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000503 ! scan attribute -relationship: has_units UO:0000010 ! second -relationship: has_units UO:0000031 ! minute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002084 -name: multidimensional chromatography modulation description -def: "Multidimensional chromatography modulation description." [PSI:MS] -is_a: MS:1000857 ! run attribute - -[Term] -id: MS:1002085 -name: two-dimensional gas chromatography with fixed modulation time -def: "Two-dimensional gas chromatography where a single modulation time is used throughout the acquisition." [PSI:MS] -is_a: MS:1002084 ! multidimensional chromatography modulation description - -[Term] -id: MS:1002086 -name: two-dimensional gas chromatography with discrete modulation time steps -def: "Two-dimensional gas chromatography where the acquisition is divided into steps, each with a different modulation time." [PSI:MS] -is_a: MS:1002084 ! multidimensional chromatography modulation description - -[Term] -id: MS:1002087 -name: two-dimensional liquid chromatography with fixed modulation time -def: "Two-dimensional liquid chromatography where a single modulation time is used throughout the acquisition." [PSI:MS] -is_a: MS:1002084 ! multidimensional chromatography modulation description - -[Term] -id: MS:1002088 -name: two-dimensional liquid chromatography with discrete modulation time steps -def: "Two-dimensional liquid chromatography where the acquisition is divided into steps, each with a different modulation time." [PSI:MS] -is_a: MS:1002084 ! multidimensional chromatography modulation description - -[Term] -id: MS:1002089 -name: ProteomeDiscoverer:Peptide Without Protein XCorr Threshold -def: "XCorr threshold for storing peptides that do not belong to a protein." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002090 -name: Calculate Probability Scores -def: "Flag indicating that a probability score for the assessment that a reported peptide match is a random occurrence is calculated." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002094 ! common search engine input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002091 -name: ProteomeDiscoverer:Maximum Delta Cn -def: "Delta Cn threshold for filtering out PSM's." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002092 -name: Percolator:Validation based on -def: "Algorithm (e.g. q-value or PEP) used for calculation of the validation score using Percolator." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002107 ! Percolator input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002093 -name: search engine input parameter -def: "Search engine input parameter." [PSI:PI] -is_a: MS:1001249 ! search input details - -[Term] -id: MS:1002094 -name: common search engine input parameter -def: "Search engine input parameter that is shared by more than one search engine." [PSI:PI] -is_a: MS:1002093 ! search engine input parameter - -[Term] -id: MS:1002095 -name: Mascot input parameter -def: "Search engine input parameters specific to Mascot." [PSI:PI, source:http://www.matrixscience.com/help/search_field_help.html] -is_a: MS:1001302 ! search engine specific input parameter - -[Term] -id: MS:1002096 -name: SEQUEST input parameter -def: "Search engine input parameters specific to SEQUEST." [PSI:PI, source:http://fields.scripps.edu/sequest/parameters.html] -is_a: MS:1001302 ! search engine specific input parameter - -[Term] -id: MS:1002097 -name: Phenyx input parameter -def: "Search engine input parameters specific to Phenyx." [PSI:PI] -is_a: MS:1001302 ! search engine specific input parameter - -[Term] -id: MS:1002098 -name: ProteinExtractor input parameter -def: "Search engine input parameters specific to ProteinExtractor." [PSI:PI] -is_a: MS:1001302 ! search engine specific input parameter - -[Term] -id: MS:1002099 -name: OMSSA input parameter -def: "Search engine input parameters specific to OMSSA." [PSI:PI] -is_a: MS:1001302 ! search engine specific input parameter - -[Term] -id: MS:1002100 -name: ProteinScape input parameter -def: "Search engine input parameters specific to ProteinScape." [PSI:PI] -is_a: MS:1001302 ! search engine specific input parameter - -[Term] -id: MS:1002101 -name: ProteomeDiscoverer input parameter -def: "Search engine input parameters specific to ProteomeDiscoverer." [PSI:PI] -is_a: MS:1001302 ! search engine specific input parameter - -[Term] -id: MS:1002103 -name: software input parameter -def: "Software input parameters." [PSI:PI] -is_a: MS:1001249 ! search input details - -[Term] -id: MS:1002104 -name: common software input parameter -def: "Software input parameter that is shared by more than one software." [PSI:PI] -is_a: MS:1002103 ! software input parameter - -[Term] -id: MS:1002105 -name: software specific input parameter -def: "Software specific input parameter." [PSI:PI] -is_a: MS:1002103 ! software input parameter - -[Term] -id: MS:1002106 -name: Scaffold input parameter -def: "Search engine input parameters specific to Scaffold." [PSI:PI] -is_a: MS:1002105 ! software specific input parameter - -[Term] -id: MS:1002107 -name: Percolator input parameter -def: "Search engine input parameters specific to Percolator." [PSI:PI] -is_a: MS:1002105 ! software specific input parameter - -[Term] -id: MS:1002108 -name: higher score better -def: "Indicates that a higher score is better." [PSI:PI] -relationship: part_of MS:1001153 ! search engine specific score - -[Term] -id: MS:1002109 -name: lower score better -def: "Indicates that a lower score is better." [PSI:PI] -relationship: part_of MS:1001153 ! search engine specific score - -[Term] -id: MS:1002110 -name: assay attribute -def: "Attribute describing an assay." [PSI:PI] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1002111 -name: assay label attribute -def: "Attribute describing an assay label." [PSI:PI] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1002112 -name: protein group list attribute -def: "Attribute describing a protein group list." [PSI:PI] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1002113 -name: protein group attribute -def: "Attribute describing a protein group." [PSI:PI] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1002114 -name: protein list attribute -def: "Attribute describing a protein list." [PSI:PI] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1002115 -name: peptide consensus list attribute -def: "Attribute describing a peptide consensus list." [PSI:PI] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1002116 -name: peptide consensus attribute -def: "Attribute describing a peptide consensus." [PSI:PI] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1002117 -name: small molecule list attribute -def: "Attribute describing a small molecule list." [PSI:PI] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1002118 -name: small molecule attribute -def: "Attribute describing a small molecule." [PSI:PI] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1002119 -name: small molecule modification attribute -def: "Attribute describing a small molecule modification." [PSI:PI] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1002120 -name: experiment name -def: "The name for identifying an experiment." [PSI:PI] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1002121 -name: spectral count feature -def: "Dummy decribing a spectral count feature." [PSI:PI] -is_a: MS:1001828 ! feature attribute - -[Term] -id: MS:1002122 -name: counts reporting -def: "FeatureList of spectral counts." [PSI:PI] -is_a: MS:1001825 ! feature list attribute - -[Term] -id: MS:1002123 -name: x-Tracker -def: "X-Tracker generic tool for quantitative proteomics." [https://bessantlab.org/software/x-tracker/] -is_a: MS:1001139 ! quantitation software name - -[Term] -id: MS:1002124 -name: ProteoSuite -def: "ProteoSuite software for the analysis of quantitative proteomics data." [DOI:10.1089/omi.2012.0022, PMID:22804616, http://www.proteosuite.org/] -is_a: MS:1001139 ! quantitation software name - -[Term] -id: MS:1002125 -name: combined FDRScore -def: "OBSOLETE FDRScore values specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PMID:19253293] -comment: This term was made obsolete because it was split into the more specific terms for PSM-level combined FDRScore (MS:1002356), distinct peptide-level combined FDRScore (MS:1002361), protein-level combined FDRScore (MS:1002366) and protein group-level combined FDRScore (MS:1002375). -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1001153 ! search engine specific score -is_obsolete: true -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002126 -name: database UniProtKB -def: "The name of the UniProtKB knowledgebase." [PSI:PI] -is_a: MS:1001013 ! database name - -[Term] -id: MS:1002127 -name: identification file attribute -def: "Attribute describing an identification file." [PSI:PI] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1002128 -name: method file format -def: "Attribute describing a method file format." [PSI:PI] -is_a: MS:1001459 ! file format - -[Term] -id: MS:1002129 -name: ITRAQAnalyzer -def: "Software for iTRAQ workflow. Extracts and normalizes iTRAQ information from an MS experiment." [http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/OpenMS-release/html/TOPP__ITRAQAnalyzer.html] -is_a: MS:1001139 ! quantitation software name -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002130 -name: identification file format -def: "Attribute describing an identification file format." [PSI:PI] -is_a: MS:1001459 ! file format - -[Term] -id: MS:1002131 -name: TOPP noise filter -def: "Noise filter component of the TOPP software." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002132 -name: TOPP NoiseFilterGaussian -def: "Removes noise from profile spectra by using a gaussian smoothing." [PSI:PI] -is_a: MS:1002131 ! TOPP noise filter - -[Term] -id: MS:1002133 -name: TOPP NoiseFilterSGolay -def: "Removes noise from profile spectra by using a Savitzky-Golay smoothing." [PSI:PI] -is_a: MS:1002131 ! TOPP noise filter - -[Term] -id: MS:1002134 -name: TOPP peak picker -def: "Peak picker component of the TOPP software." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002135 -name: TOPP PeakPickerHiRes -def: "Finds mass spectrometric peaks in high-resoluted profile mass spectra." [PSI:PI] -is_a: MS:1002134 ! TOPP peak picker - -[Term] -id: MS:1002136 -name: TOPP PeakPickerWavelet -def: "Finds mass spectrometric peaks with a wavelet algorithm in low-resoluted profile mass spectra." [PSI:PI] -is_a: MS:1002134 ! TOPP peak picker - -[Term] -id: MS:1002137 -name: TOPP spectra filter -def: "Spectra filter component of the TOPP software." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002138 -name: TOPP SpectraFilterBernNorm -def: "Applies a Bern et al normalization to peak spectra." [PMID:15262780, DOI:10.1093/bioinformatics/bth947] -is_a: MS:1002137 ! TOPP spectra filter - -[Term] -id: MS:1002139 -name: TOPP SpectraFilterMarkerMower -def: "Applies a filter to peak spectra for marked peaks." [PSI:PI] -is_a: MS:1002137 ! TOPP spectra filter - -[Term] -id: MS:1002140 -name: TOPP SpectraFilterNLargest -def: "Retains the n largest peaks of a peak spectra." [PSI:PI] -is_a: MS:1002137 ! TOPP spectra filter - -[Term] -id: MS:1002141 -name: TOPP SpectraFilterNormalizer -def: "Applies a TIC/maximal intensity normalization to peak spectra." [PSI:PI] -is_a: MS:1002137 ! TOPP spectra filter - -[Term] -id: MS:1002142 -name: TOPP SpectraFilterParentPeakMower -def: "Filters putative unfragmented precursor ions from tandem spectra." [PSI:PI] -is_a: MS:1002137 ! TOPP spectra filter - -[Term] -id: MS:1002143 -name: TOPP SpectraFilterScaler -def: "Applies a filter to peak spectra after intensity scaling according to rank." [PSI:PI] -is_a: MS:1002137 ! TOPP spectra filter - -[Term] -id: MS:1002144 -name: TOPP SpectraFilterSqrtMower -def: "Applies a filter to peak spectra after intensity scaling to the square root." [PSI:PI] -is_a: MS:1002137 ! TOPP spectra filter - -[Term] -id: MS:1002145 -name: TOPP SpectraFilterThresholdMower -def: "Applies a filter of peaks below a given threshold to peak spectra." [PSI:PI] -is_a: MS:1002137 ! TOPP spectra filter - -[Term] -id: MS:1002146 -name: TOPP SpectraFilterWindowMower -def: "Applies a filter of the largest peaks in a sliding window over a peak spectrum." [PSI:PI] -is_a: MS:1002137 ! TOPP spectra filter - -[Term] -id: MS:1002147 -name: TOPP map aligner -def: "Map aligner component of the TOPP software." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002148 -name: TOPP MapAlignerIdentification -def: "Corrects retention time distortions between maps based on common peptide identifications." [PSI:PI] -is_a: MS:1002147 ! TOPP map aligner - -[Term] -id: MS:1002149 -name: TOPP MapAlignerPoseClustering -def: "Corrects retention time distortions between maps using a pose clustering approach." [PSI:PI] -is_a: MS:1002147 ! TOPP map aligner - -[Term] -id: MS:1002150 -name: TOPP MapAlignerSpectrum -def: "Corrects retention time distortions between maps by spectrum alignment." [PSI:PI] -is_a: MS:1002147 ! TOPP map aligner - -[Term] -id: MS:1002151 -name: numerator data type attribute -def: "Attribute describing the data type of the numerator of a ratio." [PSI:PI] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1002152 -name: denominator data type attribute -def: "Attribute describing the data type of the denominator of a ratio." [PSI:PI] -is_a: MS:1001806 ! quantification object attribute - -[Term] -id: MS:1002153 -name: protein level PSM counts -def: "The number of spectra identified for this protein in spectral counting." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002738 ! protein-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002154 -name: TOPP DTAExtractor -def: "Extracts spectra of an MS run file to several files in DTA format." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002155 -name: TOPP IDMerger -def: "Merges several protein/peptide identification files into one file." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002156 -name: TOPP IDFileConverter -def: "Converts identification engine file formats." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002157 -name: TOPP SpectraMerger -def: "Merges spectra from an LC/MS map, either by precursor or by RT blocks." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002158 -name: TOPP MzTabExporter -def: "Exports various XML formats to an mzTab file." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002159 -name: TOPP MassTraceExtractor -def: "Annotates mass traces in centroided LC/MS maps." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002160 -name: TOPP PrecursorMassCorrector -def: "Correct the precursor entries of tandem MS scans." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002161 -name: TOPP HighResPrecursorMassCorrector -def: "Performs precursor mz correction on centroided high resolution data." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002162 -name: TOPP AdditiveSeries -def: "Computes an additive series to quantify a peptide in a set of samples." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002163 -name: TOPP Decharger -def: "Decharges and merges different feature charge variants of the same chemical entity." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002164 -name: TOPP EICExtractor -def: "Quantifies signals at given positions in (raw or picked) LC/MS maps." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002165 -name: TOPP feature finder -def: "Feature finder component of the TOPP software." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002166 -name: TOPP FeatureFinderCentroided -def: "Detects two-dimensional features in centroided LC-MS data." [PSI:PI] -is_a: MS:1002165 ! TOPP feature finder - -[Term] -id: MS:1002167 -name: TOPP FeatureFinderRaw -def: "Detects two-dimensional features in uncentroided LC-MS data." [PSI:PI] -is_a: MS:1002165 ! TOPP feature finder - -[Term] -id: MS:1002168 -name: TOPP FeatureFinderIsotopeWavelet -def: "Detects two-dimensional features in uncentroided LC-MS data with a wavelet algorithm." [PSI:PI] -is_a: MS:1002165 ! TOPP feature finder - -[Term] -id: MS:1002169 -name: TOPP FeatureFinderMetabo -def: "Detects two-dimensional features in centroided LC-MS data of metabolites." [PSI:PI] -is_a: MS:1002165 ! TOPP feature finder - -[Term] -id: MS:1002170 -name: TOPP FeatureFinderMRM -def: "Quantifies features LC-MS/MS MRM data." [PSI:PI] -is_a: MS:1002165 ! TOPP feature finder - -[Term] -id: MS:1002171 -name: TOPP ProteinQuantifier -def: "Computes protein abundances from annotated feature/consensus maps." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002172 -name: TOPP ConsensusMapNormalizer -def: "Normalizes maps of one consensus XML file (after linking)." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002173 -name: TOPP MapRTTransformer -def: "Applies retention time transformations to maps." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002174 -name: TOPP feature linker -def: "Feature linker component of the TOPP software." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002175 -name: TOPP FeatureLinkerLabeled -def: "Groups corresponding isotope-labeled features in a feature map." [PSI:PI] -is_a: MS:1002174 ! TOPP feature linker - -[Term] -id: MS:1002176 -name: TOPP FeatureLinkerUnlabeled -def: "Groups corresponding features from multiple maps." [PSI:PI] -is_a: MS:1002174 ! TOPP feature linker - -[Term] -id: MS:1002177 -name: TOPP FeatureLinkerUnlabeledQT -def: "Groups corresponding features from multiple maps using a quality threshold clustering approach." [PSI:PI] -is_a: MS:1002174 ! TOPP feature linker - -[Term] -id: MS:1002178 -name: TOPP CompNovo -def: "Performs a peptide/protein identification with the CompNovo engine." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002179 -name: TOPP CompNovoCID -def: "Performs a peptide/protein identification with the CompNovo engine in collision-induced dissociation (CID) mode." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002180 -name: TOPP software adaptor -def: "Software adaptor to an external program in the TOPP software." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002181 -name: TOPP InspectAdapter -def: "Identifies MS2 spectra using the external program Inspect." [PSI:PI] -is_a: MS:1002180 ! TOPP software adaptor - -[Term] -id: MS:1002182 -name: TOPP MascotAdapter -def: "Identifies MS2 spectra using the external program Mascot." [PSI:PI] -is_a: MS:1002180 ! TOPP software adaptor - -[Term] -id: MS:1002183 -name: TOPP MascotAdapterOnline -def: "Identifies MS2 spectra using the online version of the external program Mascot." [PSI:PI] -is_a: MS:1002180 ! TOPP software adaptor - -[Term] -id: MS:1002184 -name: TOPP OMSSAAdapter -def: "Identifies MS2 spectra using the external program OMSSA." [PSI:PI] -is_a: MS:1002180 ! TOPP software adaptor - -[Term] -id: MS:1002185 -name: TOPP PepNovoAdapter -def: "Identifies MS2 spectra using the external program PepNovo." [PSI:PI] -is_a: MS:1002180 ! TOPP software adaptor - -[Term] -id: MS:1002186 -name: TOPP XTandemAdapter -def: "Identifies MS2 spectra using the external program XTandem." [PSI:PI] -is_a: MS:1002180 ! TOPP software adaptor - -[Term] -id: MS:1002187 -name: TOPP SpecLibSearcher -def: "Identifies peptide MS2 spectra by spectral matching with a searchable spectral library." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002188 -name: TOPP ConsensusID -def: "Computes a consensus identification from peptide identifications of several identification engines." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002189 -name: TOPP IDConflictResolver -def: "Resolves ambiguous annotations of features with peptide identifications." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002190 -name: TOPP IDFilter -def: "Filters results from protein or peptide identification engines based on different criteria." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002191 -name: TOPP IDMapper -def: "Assigns protein/peptide identifications to feature or consensus features." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002192 -name: TOPP IDPosteriorErrorProbability -def: "Estimates posterior error probabilities using a mixture model." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002193 -name: TOPP IDRTCalibration -def: "Calibrate Retention times of peptide hits to standards." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002194 -name: TOPP PeptideIndexer -def: "Refreshes the protein references for all peptide hits." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002195 -name: TOPP PrecursorIonSelector -def: "A tool for precursor ion selection based on identification results." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002196 -name: TOPP MRMMapper -def: "MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002197 -name: TOPP OpenSwath component -def: "OpenSwath component of the TOPP software." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002198 -name: TOPP OpenSwathAnalyzer -def: "Picks peaks and finds features in an SRM experiment." [PSI:PI] -is_a: MS:1002197 ! TOPP OpenSwath component - -[Term] -id: MS:1002199 -name: TOPP OpenSwathChromatogramExtractor -def: "Extract chromatograms (XIC) from a MS2 map file." [PSI:PI] -is_a: MS:1002197 ! TOPP OpenSwath component - -[Term] -id: MS:1002200 -name: TOPP OpenSwathDecoyGenerator -def: "Generates decoys according to different models for a specific TraML." [PSI:PI] -is_a: MS:1002197 ! TOPP OpenSwath component - -[Term] -id: MS:1002201 -name: TOPP OpenSwathFeatureXMLToTSV -def: "Converts a featureXML to a mProphet tsv (tab separated values)." [PSI:PI] -is_a: MS:1002197 ! TOPP OpenSwath component - -[Term] -id: MS:1002202 -name: TOPP OpenSwathRTNormalizer -def: "Generates a transformation file for retention time space into normalized space." [PSI:PI] -is_a: MS:1002197 ! TOPP OpenSwath component - -[Term] -id: MS:1002203 -name: TOPP ProteinInference -def: "Infer proteins from a list of (high-confidence) peptides." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002204 -name: TOPP FalseDiscoveryRate -def: "Estimates the false discovery rate on peptide and protein level using decoy searches." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002205 -name: ProteoWizard msconvert -def: "Converts, filters, and processes mass spectrometry data in variety of formats." [PSI:MS] -is_a: MS:1000615 ! ProteoWizard software - -[Term] -id: MS:1002206 -name: ProteoWizard idconvert -def: "Converts, filters, and processes identifications from shotgun proteomics experiments." [PSI:MS] -is_a: MS:1000615 ! ProteoWizard software - -[Term] -id: MS:1002207 -name: ProteoWizard chainsaw -def: "Filters and processes protein sequence databases." [PSI:MS] -is_a: MS:1000615 ! ProteoWizard software - -[Term] -id: MS:1002208 -name: ProteoWizard msaccess -def: "Filters, processes, and displays mass spectrometry data in a variety of ways." [PSI:MS] -is_a: MS:1000615 ! ProteoWizard software - -[Term] -id: MS:1002209 -name: ProteoWizard SeeMS -def: "An interactive GUI application to view and filter mass spectrometry data in a variety of formats." [PSI:MS] -is_a: MS:1000615 ! ProteoWizard software - -[Term] -id: MS:1002210 -name: IsobariQ -def: "A quantitative software package designed for analysis of IPTL, TMT and iTRAQ data." [PMID:21067241, DOI:10.1021/pr1009977, http://folk.uio.no/magnusar/isobariq] -is_a: MS:1001139 ! quantitation software name -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002211 -name: Variance stabilizing normalization -def: "The model incorporates data calibration (normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation." [PMID:16646781] -is_a: MS:1001861 ! quantification data processing - -[Term] -id: MS:1002212 -name: IPTL quantitation analysis -def: "Quantification analysis using a labelling strategy where both peptide termini are labelled so that the peptides from different labelling schema are isobaric." [PSI:PI, PMID:19655813] -is_a: MS:1002009 ! isobaric label quantitation analysis - -[Term] -id: MS:1002213 -name: PAnalyzer:conclusive protein -def: "A protein identified by at least one unique (distinct, discrete) peptide (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001600 ! protein inference confidence category -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002214 -name: PAnalyzer:indistinguishable protein -def: "A member of a group of proteins sharing all peptides that are exclusive to the group (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001600 ! protein inference confidence category -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002215 -name: PAnalyzer:non-conclusive protein -def: "A protein sharing all its matched peptides with either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001600 ! protein inference confidence category -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002216 -name: PAnalyzer:ambiguous group member -def: "A protein sharing at least one peptide not matched to either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001600 ! protein inference confidence category -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002217 -name: decoy peptide -def: "A putative identified peptide issued from a decoy sequence database." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002218 -name: percent collision energy ramp start -def: "Collision energy at the start of the collision energy ramp in percent, normalized to the mass of the ion." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000138 ! normalized collision energy -relationship: has_units UO:0000187 ! percent -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002219 -name: percent collision energy ramp end -def: "Collision energy at the end of the collision energy ramp in percent, normalized to the mass of the ion." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000138 ! normalized collision energy -relationship: has_units UO:0000187 ! percent -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002220 -name: MRMaid -def: "A web-based SRM assay design tool whose transitions are generated by mining the millions of identified peptide spectra held in the EBI's PRIDE database." [PSI:PI] -is_a: MS:1000871 ! SRM software - -[Term] -id: MS:1002221 -name: MRMaid:peptide score -def: "Score in MRMaid to indicate the expected performance of the peptide in SRM." [PSI:PI] -is_a: MS:1001105 ! peptide sequence-level identification attribute -is_a: MS:1002363 ! search engine specific score for proteins - -[Term] -id: MS:1002222 -name: SRM transition attribute -def: "Attribute associated with a SRM transition." [PSI:MS] -is_a: MS:1000455 ! ion selection attribute -relationship: part_of MS:1000908 ! transition - -[Term] -id: MS:1002223 -name: precursor ion detection probability -def: "Probability of detecting precursor when parent protein is present." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002222 ! SRM transition attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002224 -name: product ion detection probability -def: "Probability of detecting product ion when precursor ion is present." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002222 ! SRM transition attribute -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002225 -name: average product ion intensity -def: "Average value of product ion intensity in a collection of identified spectra." [PSI:PI] -is_a: MS:1001226 ! product ion intensity -relationship: has_units MS:1000131 ! number of detector counts -relationship: has_units MS:1000132 ! percent of base peak -relationship: has_units MS:1000814 ! counts per second -relationship: has_units MS:1000905 ! percent of base peak times 100 - -[Term] -id: MS:1002226 -name: product ion intensity standard deviation -def: "Standard deviation of product ion intensity in a collection of identified spectra." [PSI:PI] -is_a: MS:1001226 ! product ion intensity -relationship: has_units MS:1000131 ! number of detector counts -relationship: has_units MS:1000132 ! percent of base peak -relationship: has_units MS:1000814 ! counts per second -relationship: has_units MS:1000905 ! percent of base peak times 100 - -[Term] -id: MS:1002227 -name: number of product ion observations -def: "The number of times the specific product ion has been observed in a series of SRM experiments." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002222 ! SRM transition attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002228 -name: number of precursor ion observations -def: "The number of times the specific precursor ion has been observed in a series of SRM experiments." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002222 ! SRM transition attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002229 -name: ProteomeDiscoverer:Mascot:Significance Middle -def: "Calculated relaxed significance when performing a decoy search for high-confidence peptides." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002230 -name: ProteomeDiscoverer:Mascot:Significance High -def: "Calculated relaxed significance when performing a decoy search for medium-confidence peptides." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002231 -name: regular expressions for a GUID -def: "([A-Fa-f0-9]\{8\}-([A-Fa-f0-9]\{4\}-)\{3\}[A-Fa-f0-9]\{12\})." [PSI:PI] -is_a: MS:1002479 ! regular expression - -[Term] -id: MS:1002232 -name: ProteomeDiscoverer:Default FDR calculator -def: "The default FDR calculator as globally unique identifier (GUID)." [PSI:PI] -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_regexp MS:1002231 ! regular expressions for a GUID - -[Term] -id: MS:1002233 -name: ProteomeDiscoverer:SEQUEST:Low resolution spectra contained -def: "Flag indicating if low-resolution spectra are taken into consideration." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002234 -name: selected precursor m/z -def: "Mass-to-charge ratio of a precursor ion selected for fragmentation." [PSI:PI] -synonym: "selected ion m/z" RELATED [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000455 ! ion selection attribute -relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002235 -name: ProteoGrouper:PDH score -def: "A score assigned to a single protein accession (modelled as ProteinDetectionHypothesis in mzIdentML), based on summed peptide level scores." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002236 -name: ProteoGrouper:PAG score -def: "A score assigned to a protein group (modelled as ProteinAmbiguityGroup in mzIdentML), based on all summed peptide level scores that have been assigned to the group as unique or razor peptides." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002237 -name: mzidLib -def: "A library of Java routines for manipulating mzIdentML files." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002238 -name: mzidLib:Omssa2Mzid -def: "A converter for OMSSA OMX to mzIdentML." [PSI:PI] -is_a: MS:1002237 ! mzidLib - -[Term] -id: MS:1002239 -name: mzidLib:Tandem2Mzid -def: "A converter for Tandem XML to mzIdentML." [PSI:PI] -is_a: MS:1002237 ! mzidLib - -[Term] -id: MS:1002240 -name: mzidLib:Csv2Mzid -def: "A converter for CSV files (following OMSSA CSV style) to mzIdentML." [PSI:PI] -is_a: MS:1002237 ! mzidLib - -[Term] -id: MS:1002241 -name: mzidLib:ProteoGrouper -def: "A generic and parameterizable protein inference algorithm for mzIdentML files." [PSI:PI] -is_a: MS:1002237 ! mzidLib - -[Term] -id: MS:1002242 -name: mzidLib:Thresholder -def: "A routine for keeping only identifications passing a given threshold or setting passThreshold to true or false for SpectrumIdentificationItem or ProteinDetectionHypothesis in mzIdentML files." [PSI:PI] -is_a: MS:1002237 ! mzidLib - -[Term] -id: MS:1002243 -name: mzidLib:Perform emPAI on mzid -def: "A routine for adding emPAI quantitative values to an mzIdentML file." [PSI:PI] -is_a: MS:1002237 ! mzidLib - -[Term] -id: MS:1002244 -name: mzidLib:FalseDiscoveryRate -def: "A routine for calculating local FDR, q-value and FDRScore for mzIdentML files, based on a decoy search." [PSI:PI] -is_a: MS:1002237 ! mzidLib - -[Term] -id: MS:1002245 -name: mzidLib:Mzidentml2Csv -def: "A tool for converting mzIdentML files to CSV format." [PSI:PI] -is_a: MS:1002237 ! mzidLib - -[Term] -id: MS:1002246 -name: mzidLib:CombineSearchEngines -def: "A tool for combining results analysed in parallel in two or three search engines into a single mzIdentML file." [PMID:19253293] -is_a: MS:1002237 ! mzidLib - -[Term] -id: MS:1002247 -name: mzidLib:InsertMetaDataFromFasta -def: "A tool for adding additional meta data from a FASTA file to DBSequence entries (sequence and description) in mzIdentML files." [PSI:PI] -is_a: MS:1002237 ! mzidLib - -[Term] -id: MS:1002248 -name: SEQUEST:spscore -def: "The SEQUEST result 'SpScore'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002249 -name: SEQUEST:sprank -def: "The SEQUEST result 'SpRank'." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002250 -name: SEQUEST:deltacnstar -def: "The SEQUEST result 'DeltaCnStar'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002251 -name: Comet -def: "Comet open-source sequence search engine developed at the University of Washington." [PMID:23148064] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002252 -name: Comet:xcorr -def: "The Comet result 'XCorr'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002253 -name: Comet:deltacn -def: "The Comet result 'DeltaCn'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002254 -name: Comet:deltacnstar -def: "The Comet result 'DeltaCnStar'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002255 -name: Comet:spscore -def: "The Comet result 'SpScore'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002256 -name: Comet:sprank -def: "The Comet result 'SpRank'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002257 -name: Comet:expectation value -def: "The Comet result 'Expectation value'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001153 ! search engine specific score -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002258 -name: Comet:matched ions -def: "The Comet result 'Matched Ions'." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002259 -name: Comet:total ions -def: "The Comet result 'Total Ions'." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002260 -name: PSM:FDR threshold -def: "False-discovery rate threshold for peptide-spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002483 ! PSM-level statistical threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002261 -name: Byonic -def: "Byonic search engine from Protein Metrics." [PMID:23255153] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002262 -name: Byonic:Score -def: "The Byonic score is the primary indicator of PSM correctness. The Byonic score reflects the absolute quality of the peptide-spectrum match, not the relative quality compared to other candidate peptides. Byonic scores range from 0 to about 1000, with 300 a good score, 400 a very good score, and PSMs with scores over 500 almost sure to be correct." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002263 -name: Byonic:Delta Score -def: "The drop in Byonic score from the top-scoring peptide to the next peptide with distinct sequence. In this computation, the same peptide with different modifications is not considered distinct." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002264 -name: Byonic:DeltaMod Score -def: "The drop in Byonic score from the top-scoring peptide to the next peptide different in any way, including placement of modifications. DeltaMod gives an indication of whether modifications are confidently localized; DeltaMod over 10.0 means that there is high likelihood that all modification placements are correct." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002265 -name: Byonic:PEP -def: "Byonic posterior error probability." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002266 -name: Byonic:Peptide LogProb -def: "The log p-value of the PSM. This is the log of the probability that the PSM with such a score and delta would arise by chance in a search of this size (the size of the protein database, as expanded by the modification rules). A log p-value of -3.0 should happen by chance on only one of a thousand spectra. Caveat: it is very hard to compute a p-value that works for all searches and all spectra, so read Byonic p-values with a certain amount of skepticism." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002267 -name: Byonic:Protein LogProb -def: "The log p-value of the protein." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002268 -name: Byonic:Best LogProb -def: "Best (most negative) log p-value of an individual PSM." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001116 ! single protein identification statistic -is_a: MS:1001153 ! search engine specific score -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002269 -name: Byonic:Best Score -def: "Best (largest) Byonic score of a PSM." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002270 -name: chromatography separation -def: "A technique by which molecules are separated by chemical and physical properties such as hydrophobicity or vapour pressure." [PSI:MS] -is_a: MS:1000857 ! run attribute - -[Term] -id: MS:1002271 -name: liquid chromatography separation -def: "Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid." [PSI:MS] -is_a: MS:1002270 ! chromatography separation - -[Term] -id: MS:1002272 -name: gas chromatography separation -def: "Gas chromatography (GC) is a separation technique in which the mobile phase is a gas." [PSI:MS] -is_a: MS:1002270 ! chromatography separation - -[Term] -id: MS:1002273 -name: detector potential -def: "Detector potential difference in volts." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000481 ! detector attribute -relationship: has_units UO:0000218 ! volt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002274 -name: SQ Detector 2 -def: "Waters quadrupole based SQ Detector 2." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1002275 -name: Xevo G2-S Tof -def: "Waters oa-ToF based Xevo G2-S Tof." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1002276 -name: Xevo G2-S QTof -def: "Waters oa-ToF based Xevo G2-S QTof." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1002277 -name: AutoSpec Premier -def: "Waters AutoSpec Premier magnetic sector instrument." [PSI:MS] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1002278 -name: Pegasus III -def: "LECO nominal mass resolution time-of-flight GC mass spectrometer." [PSI:MS] -is_a: MS:1001800 ! LECO instrument model - -[Term] -id: MS:1002279 -name: maXis 4G -def: "Bruker Daltonics' maXis 4G: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] -is_a: MS:1001547 ! Bruker Daltonics maXis series - -[Term] -id: MS:1002280 -name: compact -def: "Bruker Daltonics' compact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] -is_a: MS:1001536 ! Bruker Daltonics micrOTOF series - -[Term] -id: MS:1002281 -name: SRM feature level quantitation -def: "Selected Reaction Monitoring feature level quantitation." [PSI:PI] -is_a: MS:1001838 ! SRM quantitation analysis - -[Term] -id: MS:1002282 -name: SRM peptide level quantitation -def: "Selected Reaction Monitoring peptide level quantitation." [PSI:PI] -is_a: MS:1001838 ! SRM quantitation analysis - -[Term] -id: MS:1002283 -name: SRM protein level quantitation -def: "Selected Reaction Monitoring protein level quantitation." [PSI:PI] -is_a: MS:1001838 ! SRM quantitation analysis - -[Term] -id: MS:1002284 -name: SRM proteingroup level quantitation -def: "Selected Reaction Monitoring proteingroup level quantitation." [PSI:PI] -is_a: MS:1001838 ! SRM quantitation analysis - -[Term] -id: MS:1002285 -name: Trans-Proteomic Pipeline -def: "A suite of open source tools for the processing of MS2 proteomics data developed by the Seattle Proteome Center at the Institute for Systems Biology." [PSI:PI] -synonym: "TPP" EXACT [] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002286 -name: Trans-Proteomic Pipeline software -def: "A software program that is a component of the Trans-Proteomic Pipeline." [PSI:PI] -is_a: MS:1001456 ! analysis software -relationship: part_of MS:1002285 ! Trans-Proteomic Pipeline - -[Term] -id: MS:1002287 -name: PeptideProphet -def: "A program in the TPP that calculates PSM probabilities for MS2 proteomics data searched with any of the supported sequence or spectral library search engines via the pepXML format." [PMID:12403597, PMID:23176103] -is_a: MS:1002286 ! Trans-Proteomic Pipeline software - -[Term] -id: MS:1002288 -name: iProphet -def: "A program in the TPP that calculates distinct peptide probabilities based on several lines of corroborating evidence including search results from multiple search engines via the pepXML format." [PMID:21876204] -synonym: "InterProphet" EXACT [] -is_a: MS:1002286 ! Trans-Proteomic Pipeline software - -[Term] -id: MS:1002289 -name: ProteinProphet -def: "A program in the TPP that calculates protein-level probabilities based on input PSM or peptide-level probabilities from PeptideProphet or iProphet. The output is written in the protXML format." [PMID:14632076] -is_a: MS:1002286 ! Trans-Proteomic Pipeline software - -[Term] -id: MS:1002290 -name: XPRESS -def: "A program in the TPP that calculates PSM-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc." [PSI:PI] -is_a: MS:1002286 ! Trans-Proteomic Pipeline software - -[Term] -id: MS:1002291 -name: Libra -def: "A program in the TPP that calculates PSM, peptide, and protein-level abundances based on N-channel isobaric label peptide data such as iTRAQ, TMT, etc." [PSI:PI] -is_a: MS:1002286 ! Trans-Proteomic Pipeline software - -[Term] -id: MS:1002292 -name: PTMProphet -def: "A program in the TPP that calculates PTM localization probabilities by re-analyzing the peaks that are available to distinguish between possible modification sites." [PSI:PI] -is_a: MS:1002286 ! Trans-Proteomic Pipeline software - -[Term] -id: MS:1002293 -name: Bruker Daltonics SCION series -def: "Bruker Daltonics' SCION series." [PSI:MS] -is_a: MS:1000122 ! Bruker Daltonics instrument model - -[Term] -id: MS:1002294 -name: Bruker Daltonics EVOQ series -def: "Bruker Daltonics' EVOQ series." [PSI:MS] -is_a: MS:1000122 ! Bruker Daltonics instrument model - -[Term] -id: MS:1002295 -name: SCION SQ -def: "Bruker Daltonics' SCION SQ: GC-single quadrupole." [PSI:MS] -is_a: MS:1002293 ! Bruker Daltonics SCION series - -[Term] -id: MS:1002296 -name: SCION TQ -def: "Bruker Daltonics' SCION TQ: GC-triple quadrupole." [PSI:MS] -is_a: MS:1002293 ! Bruker Daltonics SCION series - -[Term] -id: MS:1002297 -name: EVOQ Elite -def: "Bruker Daltonics' EVOQ Elite: LC-triple quadrupole." [PSI:MS] -is_a: MS:1002294 ! Bruker Daltonics EVOQ series - -[Term] -id: MS:1002298 -name: EVOQ Qube -def: "Bruker Daltonics' EVOQ Qube: LC-triple quadrupole." [PSI:MS] -is_a: MS:1002294 ! Bruker Daltonics EVOQ series - -[Term] -id: MS:1002299 -name: micrOTOF-Q III -def: "Bruker Daltonics' micrOTOF-Q III: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] -is_a: MS:1001536 ! Bruker Daltonics micrOTOF series - -[Term] -id: MS:1002300 -name: amaZon Speed ETD -def: "Bruker Daltonics' amaZon Speed ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR, GC-APCI, CaptiveSpray." [PSI:MS] -is_a: MS:1001545 ! Bruker Daltonics amaZon series - -[Term] -id: MS:1002301 -name: amaZon Speed -def: "Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] -is_a: MS:1001545 ! Bruker Daltonics amaZon series - -[Term] -id: MS:1002302 -name: Bruker Container format -def: "Bruker Container raw file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1002303 -name: Bruker Container nativeID format -def: "Native identifier (UUID)." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000767 ! native spectrum identifier format -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002304 -name: domain range -def: "Domain range of a numerical value." [PSI:PI] -relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies - -[Term] -id: MS:1002305 -name: value between 0 and 1 inclusive -def: "Value range for probabilities." [PSI:PI] -is_a: MS:1002304 ! domain range - -[Term] -id: MS:1002306 -name: value greater than zero -def: "Positive value range." [PSI:PI] -is_a: MS:1002304 ! domain range - -[Term] -id: MS:1002307 -name: fragmentation ion type -def: "Type of fragment ion based on where the backbone breaks, such as a y ion or a c ion." [PSI:PI] -is_a: MS:1001221 ! product ion attribute - -[Term] -id: MS:1002308 -name: fluorescence detector -def: "A detector using a fluorescent signal after excitation with light." [PSI:MS] -is_a: MS:1000026 ! detector type - -[Term] -id: MS:1002309 -name: Byonic: Peptide AbsLogProb -def: "The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the PSM." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002310 -name: Byonic: Protein AbsLogProb -def: "The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the protein." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002311 -name: Byonic: Peptide AbsLogProb2D -def: "The absolute value of the log-base10 Byonic two-dimensional posterior error probability (PEP) of the PSM. The two-dimensional PEP takes into account protein ranking information as well as PSM information." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002312 -name: MS-Numpress linear prediction compression -def: "Compression using MS-Numpress linear prediction compression." [https://github.com/ms-numpress/ms-numpress] -is_a: MS:1000572 ! binary data compression type - -[Term] -id: MS:1002313 -name: MS-Numpress positive integer compression -def: "Compression using MS-Numpress positive integer compression." [https://github.com/ms-numpress/ms-numpress] -is_a: MS:1000572 ! binary data compression type - -[Term] -id: MS:1002314 -name: MS-Numpress short logged float compression -def: "Compression using MS-Numpress short logged float compression." [https://github.com/ms-numpress/ms-numpress] -is_a: MS:1000572 ! binary data compression type - -[Term] -id: MS:1002315 -name: consensus result -def: "Indicates a consensus result from several search engine runs." [PSI:PI] -is_a: MS:1001405 ! spectrum identification result details - -[Term] -id: MS:1002316 -name: ProteomeDiscoverer:Amanda:high confidence threshold -def: "Strict confidence probability score." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002317 -name: ProteomeDiscoverer:Amanda:middle confidence threshold -def: "Relaxed confidence probability score." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002318 -name: ProteomeDiscoverer:automatic workload -def: "Flag indicating automatic estimation of the workload level." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002319 -name: Amanda:AmandaScore -def: "The Amanda score of the scoring function for a PSM." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002320 -name: ProteomeDiscoverer:max differential modifications -def: "Maximum dynamic modifications per PSM." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002321 -name: ProteomeDiscoverer:max equal modifications -def: "Maximum equal modifications per PSM." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002322 -name: ProteomeDiscoverer:min peptide length -def: "Minimum peptide length." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002323 -name: ProteomeDiscoverer:max peptide length -def: "Maximum peptide length." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002324 -name: ProteomeDiscoverer:max number neutral loss -def: "Maximum number of same neutral losses." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002325 -name: ProteomeDiscoverer:max number neutral loss modifications -def: "Max number of same neutral losses of modifications." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002326 -name: ProteomeDiscoverer:use flanking ions -def: "Flag for usage of flanking ions." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002327 -name: ProteomeDiscoverer:max number of same modifs -def: "The maximum number of possible equal modifications per PSM." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002328 -name: ProteomeDiscoverer:perform deisotoping -def: "Defines whether a simple deisotoping shall be performed." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002329 -name: ProteomeDiscoverer:ion settings -def: "Specifies the fragment ions and neutral losses that are calculated." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002330 -name: ProteomeDiscoverer:3. Static Modification -def: "OBSOLETE ProteomeDiscoverer's 3rd static post-translational modification (PTM) input parameter." [PSI:PI] -comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002331 -name: ProteomeDiscoverer:5. Dynamic Modification -def: "OBSOLETE ProteomeDiscoverer's 5th dynamic post-translational modification (PTM) input parameter." [PSI:PI] -comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002332 -name: lab head -def: "The scientist responsible for personnel, grants, and instrumentation in a functional laboratory group." [PSI:PI] -is_a: MS:1002033 ! contact role - -[Term] -id: MS:1002333 -name: conversion software -def: "Computer software primarily designed to convert data represented in one format to another format, sometimes with minor data alterations in the process." [PSI:PI] -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002334 -name: ProCon -def: "Java software designed to convert one of several proteomics identification results formats into mzIdentML or PRIDE XML." [PSI:PI, http://www.medizinisches-proteom-center.de/procon] -is_a: MS:1002333 ! conversion software - -[Term] -id: MS:1002335 -name: PRIDE Converter2 -def: "Java software designed to convert one of several proteomics identification results formats into PRIDE XML." [PMID:22949509] -is_a: MS:1002333 ! conversion software - -[Term] -id: MS:1002336 -name: Amanda -def: "Amanda scoring system for PSM identification." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002337 -name: Andromeda -def: "Andromeda is a peptide search engine." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002338 -name: Andromeda:score -def: "The probability based score of the Andromeda search engine." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002339 -name: site:global FDR -def: "Estimation of global false discovery rate of peptides with a post-translational modification." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001405 ! spectrum identification result details -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002340 -name: ProteomeXchange project tag -def: "Tag that can be added to a ProteomeXchange dataset, to enable the grouping of datasets. One tag can be used for indicating that a given dataset is part of a bigger project, like e.g. the Human Proteome Project." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002341 -name: second-pass peptide identification -def: "A putative identified peptide found in a second-pass search of protein sequences selected from a first-pass search." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002342 -name: MZmine -def: "A framework for differential analysis of mass spectrometry data." [PMID:16403790, PMID:20650010] -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002343 -name: ion stability type -def: "OBSOLETE Stability type of the ion." [PSI:PI] -comment: This child of the former purgatory term ion was made obsolete. -is_obsolete: true - -[Term] -id: MS:1002344 -name: Maltcms -def: "Modular Application Toolkit for Chromatography Mass-Spectrometry is an application framework mainly for developers." [PSI:PI, http://maltcms.sf.net] -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002345 -name: PSM-level attribute -def: "Attribute of a single peptide-spectrum match." [PSI:PI] -is_a: MS:1002694 ! single identification result attribute - -[Term] -id: MS:1002346 -name: protein group-level identification attribute -def: "Protein group level information." [PSI:PI] -is_a: MS:1002694 ! single identification result attribute - -[Term] -id: MS:1002347 -name: PSM-level identification statistic -def: "Identification confidence metric for a peptide spectrum match." [PSI:PI] -is_a: MS:1002345 ! PSM-level attribute - -[Term] -id: MS:1002348 -name: protein group-level identification statistic -def: "Identification confidence metric for a protein group." [PSI:PI] -is_a: MS:1002346 ! protein group-level identification attribute - -[Term] -id: MS:1002349 -name: value greater than zero but less than or equal to one -def: "Positive value range less than or equal to 1." [PSI:PI] -is_a: MS:1002304 ! domain range - -[Term] -id: MS:1002350 -name: PSM-level global FDR -def: "Estimation of the global false discovery rate of peptide spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002701 ! PSM-level result list statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002351 -name: PSM-level local FDR -def: "Estimation of the local false discovery rate of peptide spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002347 ! PSM-level identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002352 -name: PSM-level p-value -def: "Estimation of the p-value for peptide spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002347 ! PSM-level identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002353 -name: PSM-level e-value -def: "Estimation of the e-value for peptide spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002347 ! PSM-level identification statistic -relationship: has_domain MS:1002306 ! value greater than zero -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002354 -name: PSM-level q-value -def: "Estimation of the q-value for peptide spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002347 ! PSM-level identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002355 -name: PSM-level FDRScore -def: "mzidLibrary FDRScore for peptide spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to 1 -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002356 -name: PSM-level combined FDRScore -def: "mzidLibrary Combined FDRScore for peptide spectrum matches specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to 1 -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002357 -name: PSM-level probability -def: "Probability that the reported peptide ion is truly responsible for some or all of the components of the specified mass spectrum." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002347 ! PSM-level identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002358 -name: search engine specific peptide sequence-level identification statistic -def: "Search engine specific distinct peptide score." [PSI:PI] -is_a: MS:1001092 ! peptide sequence-level identification statistic - -[Term] -id: MS:1002359 -name: peptide sequence-level local FDR -def: "Estimation of the local false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001092 ! peptide sequence-level identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002360 -name: distinct peptide-level FDRScore -def: "MzidLibrary FDRScore for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002361 -name: distinct peptide-level combined FDRScore -def: "Combined FDRScore for peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry) specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given peptide, used for integrating results from these distinct pools." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002362 -name: peptide sequence-level probability -def: "Probability that the reported distinct peptide sequence (irrespective of mass modifications) has been correctly identified via the referenced PSMs." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001092 ! peptide sequence-level identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002363 -name: search engine specific score for proteins -def: "Search engine specific protein scores." [PSI:PI] -is_a: MS:1001116 ! single protein identification statistic - -[Term] -id: MS:1002364 -name: protein-level local FDR -def: "Estimation of the local false discovery rate of proteins." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001116 ! single protein identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002365 -name: FDRScore for proteins -def: "MzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002366 -name: combined FDRScore for proteins -def: "MzidLibrary Combined FDRScore for proteins." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002367 -name: probability for proteins -def: "Probability that a specific protein sequence has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001116 ! single protein identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002368 -name: search engine specific score for protein groups -def: "Search engine specific protein group scores." [PSI:PI] -is_a: MS:1002348 ! protein group-level identification statistic - -[Term] -id: MS:1002369 -name: protein group-level global FDR -def: "Estimation of the global false discovery rate of protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002706 ! protein group-level result list statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002370 -name: protein group-level local FDR -def: "Estimation of the local false discovery rate of protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002348 ! protein group-level identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002371 -name: protein group-level p-value -def: "Estimation of the p-value for protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002348 ! protein group-level identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002372 -name: protein group-level e-value -def: "Estimation of the e-value for protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002348 ! protein group-level identification statistic -relationship: has_domain MS:1002306 ! value greater than zero -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002373 -name: protein group-level q-value -def: "Estimation of the q-value for protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002348 ! protein group-level identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002374 -name: protein group-level FDRScore -def: "mzidLibrary FDRScore for protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002375 -name: protein group-level combined FDRScore -def: "mzidLibrary Combined FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PMID:19253293] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002376 -name: protein group-level probability -def: "Probability that at least one of the members of a group of protein sequences has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002348 ! protein group-level identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002377 -name: ProteomeDiscoverer:Relaxed Score Threshold -def: "Specifies the threshold value for relaxed scoring." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002378 -name: ProteomeDiscoverer:Strict Score Threshold -def: "Specifies the threshold value for strict scoring." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002379 -name: ProteomeDiscoverer:Peptide Without Protein Cut Off Score -def: "Cut off score for storing peptides that do not belong to a protein." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002380 -name: false localization rate -def: "Estimation of the false localization rate for modification site assignment." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001405 ! spectrum identification result details -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002381 -name: MALDI Solutions LC-MALDI -def: "Software for automated LC-MALDI analysis and reporting." [PSI:PI] -is_a: MS:1001455 ! acquisition software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software -is_a: MS:1001557 ! Shimadzu Corporation software - -[Term] -id: MS:1002382 -name: Shimadzu MALDI-7090 -def: "Shimadzu MALDI-7090: MALDI-TOF-TOF." [PSI:PI] -is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model - -[Term] -id: MS:1002383 -name: SCiLS software -def: "SCiLS software for data acquisition and analysis." [PSI:MS] -is_a: MS:1000531 ! software - -[Term] -id: MS:1002384 -name: SCiLS Lab -def: "SCiLS Lab software." [PSI:MS] -is_a: MS:1002383 ! SCiLS software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002385 -name: SCiLS Lab format -def: "SCiLS Lab file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1002386 -name: preprocessing software -def: "Preprocessing software." [PSI:PI] -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002387 -name: PIA -def: "PIA - Protein Inference Algorithms, a toolbox for protein inference and identification analysis." [PSI:PI, http://www.medizinisches-proteom-center.de/pia] -is_a: MS:1002414 ! postprocessing software -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002388 -name: PIA XML format -def: "A compilation of search engine results in the PIA XML format." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1002389 -name: PIA workflow parameter -def: "A parameter set for a single PIA analysis." [PSI:PI] -is_a: MS:1002105 ! software specific input parameter -is_a: MS:1001302 ! search engine specific input parameter - -[Term] -id: MS:1002390 -name: PIA:FDRScore calculated -def: "Indicates whether the FDR score was calculated for the input file." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002391 -name: PIA:Combined FDRScore calculated -def: "Indicates whether the combined FDR score was calculated for the PIA compilation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002392 -name: PIA:PSM sets created -def: "Indicates whether PSM sets were created." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002393 -name: PIA:used top identifications for FDR -def: "The number of top identifications per spectrum used for the FDR calculation, 0 means all." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1002394 -name: PIA:protein score -def: "The score given to a protein by any protein inference." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002395 -name: PIA:protein inference -def: "The used algorithm for the protein inference using PIA." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002396 -name: PIA:protein inference filter -def: "A filter used by PIA for the protein inference." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002397 -name: PIA:protein inference scoring -def: "The used scoring method for the protein inference using PIA." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002398 -name: PIA:protein inference used score -def: "The used base score for the protein inference using PIA." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002399 -name: PIA:protein inference used PSMs -def: "The method to determine the PSMs used for scoring by the protein inference." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002400 -name: PIA:filter -def: "A filter used for the report generation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002389 ! PIA workflow parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002401 -name: leading protein -def: "At least one protein within each group should be annotated as a leading protein to indicate it has the strongest evidence, or approximately equal evidence as other group members." [PSI:PI] -is_a: MS:1001101 ! protein group or subset relationship - -[Term] -id: MS:1002402 -name: non-leading protein -def: "Zero to many proteins within each group should be annotated as non-leading to indicate that other proteins have stronger evidence." [PSI:PI] -is_a: MS:1001101 ! protein group or subset relationship - -[Term] -id: MS:1002403 -name: group representative -def: "An arbitrary and optional flag applied to exactly one protein per group to indicate it can serve as the representative of the group, amongst leading proteins, in effect serving as a tiebreaker for approaches that require exactly one group representative." [PSI:PI] -is_a: MS:1001101 ! protein group or subset relationship - -[Term] -id: MS:1002404 -name: count of identified proteins -def: "The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002704 ! protein-level result list attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002405 -name: protein group-level result list attribute -def: "Details describing a protein cluster." [PSI:PI] -is_a: MS:1002699 ! result list attribute - -[Term] -id: MS:1002406 -name: count of identified clusters -def: "The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file." [DOI:10.1002/pmic.201400080, PMID:25092112] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002405 ! protein group-level result list attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002407 -name: cluster identifier -def: "An identifier applied to protein groups to indicate that they are linked by shared peptides." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002698 ! protein cluster identification attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002408 -name: number of distinct protein sequences -def: "The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002405 ! protein group-level result list attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002409 -name: marginally distinguished protein -def: "Assigned to a non-leading protein that has some independent evidence to support its presence relative to the leading protein(s), e.g. the protein may have a unique peptide but not sufficient to be promoted as a leading protein of another group." [PSI:PI] -is_a: MS:1001101 ! protein group or subset relationship - -[Term] -id: MS:1002410 -name: Anubis -def: "Anubis software for selected reaction monitoring data." [PSI:PI, http://quantitativeproteomics.org/anubis] -is_a: MS:1000871 ! SRM software -is_a: MS:1001139 ! quantitation software name - -[Term] -id: MS:1002411 -name: TraML format -def: "The TraML format for transitions in SRM from the PSI. File extension '.TraML'." [PSI:PI, http://www.psidev.info/traml] -is_a: MS:1002128 ! method file format - -[Term] -id: MS:1002412 -name: total XIC area -def: "Summed area of all the extracted ion chromatogram for the peptide (e.g. of all the transitions in SRM)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002413 -name: product background -def: "The background area for the quantified transition." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002414 -name: postprocessing software -def: "Postprocessing software." [PSI:PI] -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002415 -name: protein group passes threshold -def: "A Boolean attribute to determine whether the protein group has passed the threshold indicated in the file." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002346 ! protein group-level identification attribute -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002416 -name: Orbitrap Fusion -def: "Thermo Scientific Orbitrap Fusion." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1002417 -name: Orbitrap Fusion ETD -def: "Thermo Scientific Orbitrap Fusion with ETD." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1002418 -name: TSQ Quantiva -def: "Thermo Scientific TSQ Quantiva MS." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1002419 -name: TSQ Endura -def: "Thermo Scientific TSQ Endura MS." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1002420 -name: PASSEL experiment URI -def: "URI that allows access to a PASSEL experiment." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term - -[Term] -id: MS:1002421 -name: Paragon input parameter -def: "Search engine input parameters specific to Paragon." [PSI:PI] -is_a: MS:1001302 ! search engine specific input parameter - -[Term] -id: MS:1002422 -name: Paragon: sample type -def: "The Paragon method setting indicating the type of sample at the high level, generally meaning the type of quantitation labelling or lack thereof. 'Identification' is indicated for samples without any labels for quantitation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002423 -name: Paragon: cysteine alkylation -def: "The Paragon method setting indicating the actual cysteine alkylation agent; 'None' is indicated if there was no cysteine alkylation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002424 -name: Paragon: instrument setting -def: "The Paragon method setting (translating to a large number of lower level settings) indicating the instrument used or a category of instrument." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002425 -name: Paragon: search effort -def: "The Paragon method setting that controls the two major modes of search effort of the Paragon algorithm: the Rapid mode uses a conventional database search, while the Thorough mode uses a hybrid search, starting with the same approach as the Rapid mode but then follows it with a separate tag-based approach enabling a more extensive search." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002426 -name: Paragon: ID focus -def: "A Paragon method setting that allows the inclusion of large sets of features such as biological modification or substitutions." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002427 -name: Paragon: FDR analysis -def: "The Paragon method setting that controls whether FDR analysis is conducted." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002428 -name: Paragon: quantitation -def: "The Paragon method setting that controls whether quantitation analysis is conducted." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002429 -name: Paragon: background correction -def: "The Paragon method setting that controls whether the 'Background Correction' analysis is conducted; this processing estimates a correction to the attenuation in extremity ratios that can occur in isobaric quantatitation workflows on complex samples." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002430 -name: Paragon: bias correction -def: "The Paragon method setting that controls whether 'Bias Correction' is invoked in quantitation analysis; this correction is a normalization to set the central tendency of protein ratios to unity." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002431 -name: Paragon: channel to use as denominator in ratios -def: "The Paragon method setting that controls which label channel is used as the denominator in calculating relative expression ratios." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002432 -name: search engine specific input metadata -def: "Search engine specific metadata that are not user-controlled settings." [PSI:PI] -is_a: MS:1001249 ! search input details - -[Term] -id: MS:1002433 -name: Paragon: modified data dictionary or parameter translation -def: "This metric detects if any changes have been made to the originally installed key control files for the software; if no changes have been made, then the software version and settings are sufficient to enable exact reproduction; if changes have been made, then the modified ParameterTranslation- and ProteinPilot DataDictionary-XML files much also be provided in order to exactly reproduce a result." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002432 ! search engine specific input metadata -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002434 -name: number of spectra searched -def: "Number of spectra in a search." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1001249 ! search input details -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002435 -name: data processing start time -def: "The time that a data processing action was started." [PSI:MS] -xref: value-type:xsd\:dateTime "The allowed value-type for this CV term." -is_a: MS:1000630 ! data processing parameter -relationship: has_value_type xsd\:dateTime ! The allowed value-type for this CV term - -[Term] -id: MS:1002436 -name: Paragon: digestion -def: "The Paragon method setting indicating the actual digestion agent - unlike other search tools, this setting does not include options that control partial specificity like 'semitrypsin'; if trypsin is used, trypsin is set, and partially conforming peptides are found in the Thorough mode of search; 'None' should be indicated only if there was really no digestion done." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001249 ! search input details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002437 -name: number of decoy sequences -def: "The number of decoy sequences, if the concatenated target-decoy approach is used." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." -is_a: MS:1001011 ! search database details -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1002438 -name: spectrum identification list result details -def: "Information about the list of PSMs (SpectrumIdentificationList)." [PSI:PI] -relationship: part_of MS:1001000 ! spectrum interpretation - -[Term] -id: MS:1002439 -name: final PSM list -def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult." [PSI:PI] -is_a: MS:1002438 ! spectrum identification list result details - -[Term] -id: MS:1002440 -name: intermediate PSM list -def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult." [PSI:PI] -is_a: MS:1002438 ! spectrum identification list result details - -[Term] -id: MS:1002441 -name: Andi-MS format -def: "AIA Analytical Data Interchange file format for mass spectrometry data." [PSI:PI] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1002442 -name: chromatograph file format -def: "The format of the chromatography file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format." [PSI:PI] -is_a: MS:1001459 ! file format - -[Term] -id: MS:1002443 -name: Andi-CHROM format -def: "AIA Analytical Data Interchange file format for chromatography data." [PSI:PI] -is_a: MS:1002442 ! chromatograph file format - -[Term] -id: MS:1002444 -name: 6420 Triple Quadrupole LC/MS -def: "The 6420 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002445 -name: 6460 Triple Quadrupole LC/MS -def: "The 6460 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds Agilent Jet Stream (AJS) technology to increase sensitivity." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002446 -name: 6490 Triple Quadrupole LC/MS -def: "The 6490 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds the Agilent iFunnel technology to increase sensitivity." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002447 -name: Paragon:special factor -def: "The Paragon method setting indicating a list of one or more 'special factors', which generally capture secondary effects (relative to other settings) as a set of probabilities of modification features that override the assumed levels. For example the 'gel-based ID' special factor causes an increase probability of oxidation on several resides because of the air exposure impact on a gel, in addition to other effects." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002421 ! Paragon input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002448 -name: PEAKS:inChorusPeptideScore -def: "The PEAKS inChorus peptide score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002449 -name: PEAKS:inChorusProteinScore -def: "The PEAKS inChorus protein score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002450 -name: param: b ion-H3PO4 DEPRECATED -def: "Ion b-H3PO4: b ion with lost phosphoric acid." [PSI:PI] -is_a: MS:1001066 ! ions series considered in search - -[Term] -id: MS:1002451 -name: param: y ion-H3PO4 DEPRECATED -def: "Ion y-H3PO4: y ion with lost phosphoric acid." [PSI:PI] -is_a: MS:1001066 ! ions series considered in search - -[Term] -id: MS:1002452 -name: Maui -def: "The Maltcms Graphical User Interface." [PSI:PI, http://maltcms.sf.net] -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002453 -name: No fixed modifications searched -def: "No fixed modifications are included as a parameter for the search, and therefore they are not reported." [PSI:PI] -is_a: MS:1002094 ! common search engine input parameter - -[Term] -id: MS:1002454 -name: No variable modifications searched -def: "No variable modifications are included as a parameter for the search, and therefore they are not reported." [PSI:PI] -is_a: MS:1002094 ! common search engine input parameter - -[Term] -id: MS:1002455 -name: H2O neutral loss -def: "OBSOLETE Neutral loss of water." [PSI:PI] -comment: This term was obsoleted because it should be replaced by MS:1000336 with value H2O. -is_a: MS:1000336 ! neutral loss -is_a: MS:1002473 ! ion series considered in search -is_obsolete: true - -[Term] -id: MS:1002456 -name: NH3 neutral loss -def: "OBSOLETE Neutral loss of ammonia." [PSI:PI] -comment: This term was obsoleted because it should be replaced by MS:1000336 with value NH3. -is_a: MS:1000336 ! neutral loss -is_a: MS:1002473 ! ion series considered in search -is_obsolete: true - -[Term] -id: MS:1002457 -name: H3PO4 neutral loss -def: "OBSOLETE Neutral loss of phosphoric acid." [PSI:PI] -comment: This term was obsoleted because it should be replaced by MS:1000336 with value H3PO4. -is_a: MS:1000336 ! neutral loss -is_a: MS:1002473 ! ion series considered in search -is_obsolete: true - -[Term] -id: MS:1002458 -name: PeptideShaker -def: "PeptideShaker is a software for the interpretation of proteomics identification results." [PSI:PI, http://peptide-shaker.googlecode.com] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002459 -name: MS Amanda csv format -def: "MS Amanda csv output format." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1002460 -name: protein group-level global FNR -def: "Estimation of the global false negative rate of protein groups." [PSI:PI] -is_a: MS:1002706 ! protein group-level result list statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive - -[Term] -id: MS:1002461 -name: protein group-level confidence -def: "Estimation of the global confidence of protein groups." [PSI:PI] -is_a: MS:1002348 ! protein group-level identification statistic - -[Term] -id: MS:1002462 -name: peptide sequence-level global FNR -def: "Estimation of the global false negative rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] -is_a: MS:1002703 ! peptide sequence-level result list statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive - -[Term] -id: MS:1002463 -name: peptide sequence-level global confidence -def: "Estimation of the global confidence for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] -is_a: MS:1002703 ! peptide sequence-level result list statistic - -[Term] -id: MS:1002464 -name: PSM-level global FNR -def: "Estimation of the global false negative rate of peptide spectrum matches." [PSI:PI] -is_a: MS:1002701 ! PSM-level result list statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive - -[Term] -id: MS:1002465 -name: PSM-level global confidence -def: "Estimation of the global confidence of peptide spectrum matches." [PSI:PI] -is_a: MS:1002701 ! PSM-level result list statistic - -[Term] -id: MS:1002466 -name: PeptideShaker PSM score -def: "The probability based PeptideShaker PSM score." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002467 -name: PeptideShaker PSM confidence -def: "The probability based PeptideShaker PSM confidence." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002468 -name: PeptideShaker peptide score -def: "The probability based PeptideShaker peptide score." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002469 -name: PeptideShaker peptide confidence -def: "The probability based PeptideShaker peptide confidence." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002470 -name: PeptideShaker protein group score -def: "The probability based PeptideShaker protein group score." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002471 -name: PeptideShaker protein group confidence -def: "The probability based PeptideShaker protein group confidence." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002472 -name: trap-type collision-induced dissociation -def: "A collision-induced dissociation process that occurs in a trap-type collision cell." [PSI:PI] -is_a: MS:1000133 ! collision-induced dissociation - -[Term] -id: MS:1002473 -name: ion series considered in search -def: "The description of the ion fragment series (including charges and neutral losses) that are considered by the search engine." [PSI:PI] -is_a: MS:1001249 ! search input details - -[Term] -id: MS:1002474 -name: ProteoAnnotator:non-canonical gene model score -def: "The sum of peptide-level scores for peptides mapped only to non-canonical gene models within the group." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002475 -name: ProteoAnnotator:count alternative peptides -def: "The count of the number of peptide sequences mapped to non-canonical gene models only within the group." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002476 -name: ion mobility drift time -def: "Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000455 ! ion selection attribute -is_a: MS:1002892 ! ion mobility attribute -relationship: has_units UO:0000028 ! millisecond -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002477 -name: mean ion mobility drift time array -def: "Array of population mean ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002893 ! ion mobility array -relationship: has_units UO:0000028 ! millisecond -relationship: has_units UO:0000010 ! second -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002478 -name: mean charge array -def: "Array of mean charge values where the mean charge is calculated as a weighted mean of the charges of individual peaks that are aggregated into a processed spectrum." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -is_a: MS:1000513 ! binary data array - -[Term] -id: MS:1002479 -name: regular expression -def: "Regular expression." [PSI:PI] -relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies - -[Term] -id: MS:1002480 -name: regular expression for a digital object identifier (DOI) -def: "(10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+)." [PSI:PI, http://dx.doi.org/] -is_a: MS:1002479 ! regular expression - -[Term] -id: MS:1002481 -name: higher energy beam-type collision-induced dissociation -def: "A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV." [PSI:MS] -is_a: MS:1000422 ! beam-type collision-induced dissociation - -[Term] -id: MS:1002482 -name: statistical threshold -def: "Estimated statistical threshold." [PSI:MS] -is_a: MS:1001060 ! quality estimation method details - -[Term] -id: MS:1002483 -name: PSM-level statistical threshold -def: "Estimated statistical threshold at PSM-level." [PSI:MS] -is_a: MS:1002573 ! spectrum identification statistical threshold - -[Term] -id: MS:1002484 -name: peptide-level statistical threshold -def: "Estimated statistical threshold at peptide-level." [PSI:MS] -is_a: MS:1002573 ! spectrum identification statistical threshold - -[Term] -id: MS:1002485 -name: protein-level statistical threshold -def: "Estimated statistical threshold at protein-level." [PSI:MS] -is_a: MS:1002572 ! protein detection statistical threshold - -[Term] -id: MS:1002486 -name: protein group-level statistical threshold -def: "Estimated statistical threshold at protein group-level." [PSI:PI] -is_a: MS:1002572 ! protein detection statistical threshold - -[Term] -id: MS:1002487 -name: MassIVE dataset identifier -def: "Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002488 -name: MassIVE dataset URI -def: "URI that allows the access to one dataset in the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term - -[Term] -id: MS:1002489 -name: special processing -def: "Details describing a special processing." [PSI:PI] -is_a: MS:1001080 ! search type -relationship: part_of MS:1001000 ! spectrum interpretation - -[Term] -id: MS:1002490 -name: peptide-level scoring -def: "Peptide-level scoring performed." [PSI:PI] -is_a: MS:1002489 ! special processing - -[Term] -id: MS:1002491 -name: modification localization scoring -def: "Modification localization scoring performed." [PSI:PI] -is_a: MS:1002489 ! special processing - -[Term] -id: MS:1002492 -name: consensus scoring -def: "Consensus multiple search engine approach performed." [PSI:PI] -is_a: MS:1002489 ! special processing - -[Term] -id: MS:1002493 -name: sample pre-fractionation -def: "Sample pre-fractionation performed." [PSI:PI] -is_a: MS:1002489 ! special processing - -[Term] -id: MS:1002494 -name: cross-linking search -def: "Cross-linking search performed." [PSI:PI] -is_a: MS:1002489 ! special processing - -[Term] -id: MS:1002495 -name: no special processing -def: "No special processing performed." [PSI:PI] -is_a: MS:1002489 ! special processing - -[Term] -id: MS:1002496 -name: group PSMs by sequence -def: "Group PSMs by distinct peptide sequence ignoring modifications." [PSI:PI] -is_a: MS:1002658 ! identification parameter - -[Term] -id: MS:1002497 -name: group PSMs by sequence with modifications -def: "Group PSMs by distinct peptide sequence with taking modifications into account." [PSI:PI] -is_a: MS:1002658 ! identification parameter - -[Term] -id: MS:1002498 -name: group PSMs by sequence with modifications and charge -def: "Group PSMs by distinct peptide sequence with taking modifications and charge into account." [PSI:PI] -is_a: MS:1002658 ! identification parameter - -[Term] -id: MS:1002499 -name: peptide level score -def: "OBSOLETE Peptide level score." [PSI:PI] -comment: This term was obsoleted because it was never intended to go in the CV. -is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -is_obsolete: true - -[Term] -id: MS:1002500 -name: peptide passes threshold -def: "A Boolean attribute to determine whether the peptide has passed the threshold indicated in the file." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002501 -name: no PSM threshold -def: "Indicating that no PSM threshold was used." [PSI:PI] -is_a: MS:1002701 ! PSM-level result list statistic - -[Term] -id: MS:1002502 -name: no peptide-level threshold -def: "Indicating that no peptide-level threshold was used." [PSI:PI] -is_a: MS:1001105 ! peptide sequence-level identification attribute - -[Term] -id: MS:1002503 -name: PSM is used for peptide-level scoring -def: "Flags a PSM that it is used for peptide-level scoring." [PSI:PI] -is_a: MS:1001105 ! peptide sequence-level identification attribute - -[Term] -id: MS:1002504 -name: modification index -def: "The order of modifications to be referenced elsewhere in the document." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1001055 ! modification parameters -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002505 -name: regular expression for modification localization scoring -def: "([:digit:]+:[0|1]\{1\}.[:digit:]+[Ee]{0,1}[+-]{0,1}[:digit:]*:[:digit:]+[|]\{1\}[:digit:]+:(true|false)\{1\})." [PSI:PI] -is_a: MS:1002479 ! regular expression - -[Term] -id: MS:1002506 -name: modification position score -def: "Modification position score." [PSI:PI] -is_a: MS:1001055 ! modification parameters - -[Term] -id: MS:1002507 -name: modification rescoring:false localization rate -def: "Mod position score: false localization rate." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002506 ! modification position score -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002508 -name: cross-linking attribute -def: "Cross-linking attribute." [PSI:PI] -is_a: MS:1002694 ! single identification result attribute - -[Term] -id: MS:1002509 -name: cross-link donor -def: "The Cross-linking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002508 ! cross-linking attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002510 -name: cross-link acceptor -def: "Cross-linking acceptor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002508 ! cross-linking attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002511 -name: cross-link spectrum identification item -def: "Cross-linked spectrum identification item." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002508 ! cross-linking attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002512 -name: cross-linking score -def: "Cross-linking scoring value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002513 -name: molecules per cell -def: "The absolute abundance of protein in a cell." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002514 -name: absolute quantitation analysis -def: "Absolute quantitation analysis." [PSI:PI] -is_a: MS:1001833 ! quantitation analysis summary - -[Term] -id: MS:1002515 -name: internal peptide reference used -def: "States whether an internal peptide reference is used or not in absolute quantitation analysis." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001832 ! quantitation software comment or customizations -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002516 -name: internal protein reference used -def: "States whether an internal protein reference is used or not in absolute quantitation analysis." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1001832 ! quantitation software comment or customizations -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002517 -name: internal reference abundance -def: "The absolute abundance of the spiked in reference peptide or protein used for absolute quantitation analysis." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002518 -name: Progenesis:protein group normalised abundance -def: "The data type normalised abundance for protein groups produced by Progenesis LC-MS." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002739 ! protein group-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002519 -name: Progenesis:protein group raw abundance -def: "The data type raw abundance for protein groups produced by Progenesis LC-MS." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002739 ! protein group-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002520 -name: peptide group ID -def: "Peptide group identifier for peptide-level stats." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001105 ! peptide sequence-level identification attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002521 -name: mass spectrometry imaging -def: "A technique in which mass spectra are acquired in a spatially resolved manner. This is typically achieved by scanning a laser or primary ion beam over a sample and acquiring a mass spectrum at each position." [PSI:PI] -is_a: MS:1000857 ! run attribute - -[Term] -id: MS:1002522 -name: ProteomeDiscoverer:1. Static Terminal Modification -def: "Determine 1st static terminal post-translational modifications (PTMs)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002523 -name: Q Exactive HF -def: "Thermo Scientific Q Exactive." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1002524 -name: PepFinder -def: "Thermo Scientific PepFinder BioPharma analysis software." [PSI:PI] -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002525 -name: TSQ 8000 Evo -def: "Thermo Scientific TSQ 8000 Evo MS." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1002526 -name: Exactive Plus -def: "Thermo Scientific Exactive Plus MS." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1002527 -name: instrument specific scan attribute -def: "Instrument specific scan properties that are associated with a value." [PSI:PI] -is_a: MS:1000503 ! scan attribute - -[Term] -id: MS:1002528 -name: synchronous prefilter selection -def: "Synchronous prefilter selection." [PSI:PI] -synonym: "SPS" EXACT [] -is_a: MS:1002527 ! instrument specific scan attribute - -[Term] -id: MS:1002529 -name: resolution array -def: "A data array of resolution values." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000523 "64-bit float" -is_a: MS:1000513 ! binary data array - -[Term] -id: MS:1002530 -name: baseline array -def: "A data array of signal baseline values (the signal in the absence of analytes)." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000523 "64-bit float" -is_a: MS:1000513 ! binary data array - -[Term] -id: MS:1002531 -name: UIMF format -def: "SQLite-based file format created at Pacific Northwest National Lab. It stores an intermediate analysis of ion-mobility mass spectrometry data." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1002532 -name: UIMF nativeID format -def: "Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger frameType=xsd:nonNegativeInteger." [PSI:MS] -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1002533 -name: TripleTOF 6600 -def: "SCIEX TripleTOF 6600, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002534 -name: ProLuCID:xcorr -def: "The ProLuCID result 'XCorr'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002535 -name: ProLuCID:deltacn -def: "The ProLuCID result 'DeltaCn'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002536 -name: D-Score -def: "D-Score for PTM site location at the PSM-level." [PMID:23307401] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002537 -name: MD-Score -def: "MD-Score for PTM site location at the PSM-level." [PMID:21057138] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002538 -name: PTM localization confidence metric -def: "Localization confidence metric for a post translational modification (PTM)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001405 ! spectrum identification result details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002539 -name: PeptideShaker PTM confidence type -def: "PeptideShaker quality criteria for the confidence of PTM localizations." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002538 ! PTM localization confidence metric -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002540 -name: PeptideShaker PSM confidence type -def: "PeptideShaker quality criteria for the confidence of PSM's." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002347 ! PSM-level identification statistic -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002541 -name: PeptideShaker peptide confidence type -def: "PeptideShaker quality criteria for the confidence of peptide identifications." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002542 -name: PeptideShaker protein confidence type -def: "PeptideShaker quality criteria for the confidence of protein identifications." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001116 ! single protein identification statistic -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002543 -name: xiFDR -def: "Target/Decoy based FDR estimation for cross-linking peptide-identifications." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002544 -name: xi -def: "Search engine for cross-linked peptides." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002545 -name: xi:score -def: "The xi result 'Score'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002546 -name: Skyline mzQuantML converter -def: "A software package to convert Skyline report to mzQuantML." [PSI:PI, http://code.google.com/p/srm-mzquantml-convertor/] -is_a: MS:1001139 ! quantitation software name -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002547 -name: normalized spectral abundance factor -def: "A normalized spectral abundance factor (NSAF)." [DOI:10.1021/pr060161n, PMID:16944946] -is_a: MS:1001805 ! quantification datatype - -[Term] -id: MS:1002548 -name: distributed normalized spectral abundance factor -def: "A distributed normalized spectral abundance factor (dNSAF)." [DOI:10.1021/ac9023999, PMID:20166708] -is_a: MS:1001805 ! quantification datatype - -[Term] -id: MS:1002549 -name: PTM localization distinct peptide-level statistic -def: "Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence." [PSI:PI] -is_a: MS:1002689 ! PTM localization single result statistic - -[Term] -id: MS:1002550 -name: peptide:phosphoRS score -def: "phosphoRS score for PTM site location at the peptide-level." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002549 ! PTM localization distinct peptide-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002551 -name: peptide:Ascore -def: "A-score for PTM site location at the peptide-level." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002549 ! PTM localization distinct peptide-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002552 -name: peptide:H-Score -def: "H-Score for peptide phosphorylation site location at the peptide-level." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002549 ! PTM localization distinct peptide-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002553 -name: peptide:D-Score -def: "D-Score for PTM site location at the peptide-level." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002549 ! PTM localization distinct peptide-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002554 -name: peptide:MD-Score -def: "MD-Score for PTM site location at the peptide-level." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002549 ! PTM localization distinct peptide-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002555 -name: PTM localization score threshold -def: "Threshold for PTM site location score." [PSI:PI] -is_a: MS:1001405 ! spectrum identification result details - -[Term] -id: MS:1002556 -name: Ascore threshold -def: "Threshold for Ascore PTM site location score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002557 -name: D-Score threshold -def: "Threshold for D-score PTM site location score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002558 -name: MD-Score threshold -def: "Threshold for MD-score PTM site location score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002559 -name: H-Score threshold -def: "Threshold for H-score PTM site location score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002560 -name: DeBunker:score threshold -def: "Threshold for DeBunker PTM site location score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002561 -name: Mascot:PTM site assignment confidence threshold -def: "Threshold for Mascot PTM site assignment confidence." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002562 -name: MSQuant:PTM-score threshold -def: "Threshold for MSQuant:PTM-score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002563 -name: MaxQuant:PTM Score threshold -def: "Threshold for MaxQuant:PTM Score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002564 -name: MaxQuant:P-site localization probability threshold -def: "Threshold for MaxQuant:P-site localization probability." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002565 -name: MaxQuant:PTM Delta Score threshold -def: "Threshold for MaxQuant:PTM Delta Score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002566 -name: MaxQuant:Phospho (STY) Probabilities threshold -def: "Threshold for MaxQuant:Phospho (STY) Probabilities." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002567 -name: phosphoRS score threshold -def: "Threshold for phosphoRS score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002568 -name: phosphoRS site probability threshold -def: "Threshold for phosphoRS site probability." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002569 -name: ProteomeDiscoverer:Number of Spectra Processed At Once -def: "Number of spectra processed at once in a ProteomeDiscoverer search." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002101 ! ProteomeDiscoverer input parameter -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002570 -name: sequence multiply subsumable protein -def: "A protein for which the matched peptide sequences are the same, or a subset of, the matched peptide sequences for two or more other proteins combined. These other proteins need not all be in the same group." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002571 -name: spectrum multiply subsumable protein -def: "A protein for which the matched spectra are the same, or a subset of, the matched spectra for two or more other proteins combined. These other proteins need not all be in the same group." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001101 ! protein group or subset relationship -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002572 -name: protein detection statistical threshold -def: "Estimated statistical threshold used for protein detection." [PSI:MS] -is_a: MS:1002482 ! statistical threshold - -[Term] -id: MS:1002573 -name: spectrum identification statistical threshold -def: "Estimated statistical threshold used for spectrum identification." [PSI:MS] -is_a: MS:1002482 ! statistical threshold - -[Term] -id: MS:1002574 -name: ASAPRatio -def: "A program in the TPP that calculates PSM, peptide, and protein-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc." [PSI:PI] -is_a: MS:1002286 ! Trans-Proteomic Pipeline software - -[Term] -id: MS:1002575 -name: Tide -def: "Tide open-source sequence search program developed at the University of Washington." [PMID:21761931] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002576 -name: Andromeda result format -def: "Andromeda result file output format." [PSI:PI] -is_a: MS:1001040 ! intermediate analysis format - -[Term] -id: MS:1002577 -name: 2000 QTRAP -def: "SCIEX 2000 QTRAP." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002578 -name: 2500 QTRAP -def: "SCIEX 2500 QTRAP." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002579 -name: 3500 QTRAP -def: "SCIEX 3500 QTRAP." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002580 -name: QTRAP 4500 -def: "SCIEX QTRAP 4500." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002581 -name: QTRAP 6500 -def: "SCIEX QTRAP 6500." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002582 -name: QTRAP 6500+ -def: "SCIEX QTRAP 6500+." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002583 -name: TripleTOF 4600 -def: "SCIEX TripleTOF 4600 time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002584 -name: TripleTOF 5600+ -def: "SCIEX TripleTOF 5600+ time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002585 -name: API 100 -def: "Applied Biosystems/MDS SCIEX API 100 MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002586 -name: API 100LC -def: "Applied Biosystems/MDS SCIEX API 100LC MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002587 -name: API 165 -def: "Applied Biosystems/MDS SCIEX API 165 MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002588 -name: API 300 -def: "Applied Biosystems/MDS SCIEX API 300 MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002589 -name: API 350 -def: "Applied Biosystems/MDS SCIEX API 350 MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002590 -name: API 365 -def: "Applied Biosystems/MDS SCIEX API 365 MS." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002591 -name: Triple Quad 3500 -def: "SCIEX Triple Quad 3500." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002592 -name: Triple Quad 4500 -def: "SCIEX Triple Quad 4500." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002593 -name: Triple Quad 5500 -def: "SCIEX Triple Quad 5500." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002594 -name: Triple Quad 6500 -def: "SCIEX Triple Quad 6500." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002595 -name: Triple Quad 6500+ -def: "SCIEX Triple Quad 6500+." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002596 -name: ProLuCID -def: "The SEQUEST-like sequence search engine ProLuCID, developed in the Yates Lab at the Scripps Research Institute." [PMID:26171723] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002597 -name: MS1 format -def: "MS1 file format for MS1 spectral data." [PMID:15317041, DOI:10.1002/rcm.1603] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1002598 -name: DTASelect -def: "Analysis software designed to reassemble the SEQUEST peptide identifications and to highlight the most significant matches." [PMID:12643522, http://fields.scripps.edu/DTASelect/] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002599 -name: splash key -def: "Spectral Hash key, an unique identifier for spectra." [PMID:27824832] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001405 ! spectrum identification result details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002600 -name: PRIDE XML -def: "Internal data and submission format of the PRIDE database." [http://ftp.pride.ebi.ac.uk/pride/resources/schema/pride/pride.xsd] -is_a: MS:1002130 ! identification file format -is_a: MS:1001405 ! spectrum identification result details - -[Term] -id: MS:1002601 -name: mzTab -def: "Tabular result format for proteomics and metabolomics experiments." [PMID:24980485, http://www.psidev.info/mztab/] -is_a: MS:1000914 ! tab delimited text format - -[Term] -id: MS:1002602 -name: sample label -def: "Reagent used in labeled quantification methods." [PSI:PI] -is_a: MS:1002111 ! assay label attribute -is_a: MS:1000548 ! sample attribute - -[Term] -id: MS:1002603 -name: ICAT reagent -def: "Isotope coded affinity tag reagent." [PSI:PI] -is_a: MS:1002602 ! sample label - -[Term] -id: MS:1002604 -name: ICAT heavy reagent -def: "The name of the sample labelled with the heavy ICAT label." [PSI:PI] -is_a: MS:1002603 ! ICAT reagent - -[Term] -id: MS:1002605 -name: ICAT light reagent -def: "The name of the sample labelled with the light ICAT label." [PSI:PI] -is_a: MS:1002603 ! ICAT reagent - -[Term] -id: MS:1002606 -name: ICPL reagent -def: "Isotope coded protein labeling reagent." [PSI:PI] -is_a: MS:1002602 ! sample label - -[Term] -id: MS:1002607 -name: ICPL reagent 0 -def: "The name of the sample labelled with the ICPL reagent 0." [PSI:PI] -is_a: MS:1002606 ! ICPL reagent - -[Term] -id: MS:1002608 -name: ICPL reagent 4 -def: "The name of the sample labelled with the ICPL reagent 4." [PSI:PI] -is_a: MS:1002606 ! ICPL reagent - -[Term] -id: MS:1002609 -name: ICPL reagent 6 -def: "The name of the sample labelled with the ICPL reagent 6." [PSI:PI] -is_a: MS:1002606 ! ICPL reagent - -[Term] -id: MS:1002610 -name: ICPL reagent 10 -def: "The name of the sample labelled with the ICPL reagent 10." [PSI:PI] -is_a: MS:1002606 ! ICPL reagent - -[Term] -id: MS:1002611 -name: SILAC reagent -def: "Stable isotope labeling with amino acids in cell culture reagent." [PSI:PI] -is_a: MS:1002602 ! sample label - -[Term] -id: MS:1002612 -name: SILAC heavy reagent -def: "The name of the sample labelled with the heavy SILAC label." [PSI:PI] -is_a: MS:1002611 ! SILAC reagent - -[Term] -id: MS:1002613 -name: SILAC medium reagent -def: "The name of the sample labelled with the medium SILAC label." [PSI:PI] -is_a: MS:1002611 ! SILAC reagent - -[Term] -id: MS:1002614 -name: SILAC light reagent -def: "The name of the sample labelled with the light SILAC label." [PSI:PI] -is_a: MS:1002611 ! SILAC reagent - -[Term] -id: MS:1002615 -name: TMT reagent -def: "Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT or hydrazideTMT isobaric labeling." [PSI:PI] -is_a: MS:1002602 ! sample label - -[Term] -id: MS:1002616 -name: TMT reagent 126 -def: "The name of the sample labelled with the TMT reagent 126." [PSI:PI] -is_a: MS:1002615 ! TMT reagent - -[Term] -id: MS:1002617 -name: TMT reagent 127 -def: "The name of the sample labelled with the TMT reagent 127." [PSI:PI] -is_a: MS:1002615 ! TMT reagent - -[Term] -id: MS:1002618 -name: TMT reagent 128 -def: "The name of the sample labelled with the TMT reagent 128." [PSI:PI] -is_a: MS:1002615 ! TMT reagent - -[Term] -id: MS:1002619 -name: TMT reagent 129 -def: "The name of the sample labelled with the TMT reagent 129." [PSI:PI] -is_a: MS:1002615 ! TMT reagent - -[Term] -id: MS:1002620 -name: TMT reagent 130 -def: "The name of the sample labelled with the TMT reagent 130." [PSI:PI] -is_a: MS:1002615 ! TMT reagent - -[Term] -id: MS:1002621 -name: TMT reagent 131 -def: "The name of the sample labelled with the TMT reagent 131." [PSI:PI] -is_a: MS:1002615 ! TMT reagent - -[Term] -id: MS:1002622 -name: iTRAQ reagent -def: "Isobaric tag for relative and absolute quantitation (iTRAQ or iTRAQH) reagent." [PSI:PI] -is_a: MS:1002602 ! sample label - -[Term] -id: MS:1002623 -name: iTRAQ reagent 113 -def: "The name of the sample labelled with the iTRAQ reagent 113." [PSI:PI] -is_a: MS:1002622 ! iTRAQ reagent - -[Term] -id: MS:1002624 -name: iTRAQ reagent 114 -def: "The name of the sample labelled with the iTRAQ reagent 114." [PSI:PI] -is_a: MS:1002622 ! iTRAQ reagent - -[Term] -id: MS:1002625 -name: iTRAQ reagent 115 -def: "The name of the sample labelled with the iTRAQ reagent 115." [PSI:PI] -is_a: MS:1002622 ! iTRAQ reagent - -[Term] -id: MS:1002626 -name: iTRAQ reagent 116 -def: "The name of the sample labelled with the iTRAQ reagent 116." [PSI:PI] -is_a: MS:1002622 ! iTRAQ reagent - -[Term] -id: MS:1002627 -name: iTRAQ reagent 117 -def: "The name of the sample labelled with the iTRAQ reagent 117." [PSI:PI] -is_a: MS:1002622 ! iTRAQ reagent - -[Term] -id: MS:1002628 -name: iTRAQ reagent 118 -def: "The name of the sample labelled with the iTRAQ reagent 118." [PSI:PI] -is_a: MS:1002622 ! iTRAQ reagent - -[Term] -id: MS:1002629 -name: iTRAQ reagent 119 -def: "The name of the sample labelled with the iTRAQ reagent 119." [PSI:PI] -is_a: MS:1002622 ! iTRAQ reagent - -[Term] -id: MS:1002630 -name: iTRAQ reagent 121 -def: "The name of the sample labelled with the iTRAQ reagent 121." [PSI:PI] -is_a: MS:1002622 ! iTRAQ reagent - -[Term] -id: MS:1002631 -name: Electron-Transfer/Higher-Energy Collision Dissociation (EThcD) -def: "A dissociation process combining electron-transfer and higher-energy collision dissociation (EThcD). It combines ETD (reaction time) followed by HCD (activation energy)." [PSI:PI] -synonym: "EThcD" EXACT [] -is_a: MS:1000044 ! dissociation method - -[Term] -id: MS:1002632 -name: jPOST dataset identifier -def: "Dataset identifier issued by the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002633 -name: jPOST dataset URI -def: "URI that allows the access to one dataset in the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term - -[Term] -id: MS:1002634 -name: Q Exactive Plus -def: "Thermo Scientific Q Exactive Plus." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1002635 -name: proteogenomics search -def: "Proteogenomics search performed." [PSI:PI] -is_a: MS:1002489 ! special processing - -[Term] -id: MS:1002636 -name: proteogenomics attribute -def: "Proteogenomics attribute." [PSI:PI] -is_a: MS:1001105 ! peptide sequence-level identification attribute - -[Term] -id: MS:1002637 -name: chromosome name -def: "The name or number of the chromosome to which a given peptide has been mapped." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002636 ! proteogenomics attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002638 -name: chromosome strand -def: "The strand (+ or -) to which the peptide has been mapped." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002636 ! proteogenomics attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002639 -name: peptide start on chromosome -def: "OBSOLETE The overall start position on the chromosome to which a peptide has been mapped i.e. the position of the first base of the first codon, using a zero-based counting system." [PSI:PI] -comment: This term was obsoleted because it contains redundant info contained in term MS:1002643 - peptide start positions on chromosome. -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002636 ! proteogenomics attribute -is_obsolete: true -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002640 -name: peptide end on chromosome -def: "The overall end position on the chromosome to which a peptide has been mapped i.e. the position of the third base of the last codon, using a zero-based counting system." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002636 ! proteogenomics attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002641 -name: peptide exon count -def: "The number of exons to which the peptide has been mapped." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002636 ! proteogenomics attribute -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002642 -name: peptide exon nucleotide sizes -def: "A comma separated list of the number of DNA bases within each exon to which a peptide has been mapped. Assuming standard operation of a search engine, the peptide exon sizes should sum to exactly three times the peptide length." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002636 ! proteogenomics attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002643 -name: peptide start positions on chromosome -def: "A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002636 ! proteogenomics attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002644 -name: genome reference version -def: "The reference genome and versioning string as used for mapping. All coordinates are within this frame of reference." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002636 ! proteogenomics attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002645 -name: MSDK -def: "Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing of mass spectrometry data." [PSI:PI, http://msdk.github.io/] -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002646 -name: native spectrum identifier format, combined spectra -def: "Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formated." [PSI:PI] -synonym: "nativeID format, combined spectra" EXACT [] -relationship: part_of MS:1000577 ! source data file - -[Term] -id: MS:1002647 -name: Thermo nativeID format, combined spectra -def: "Thermo comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002648 -name: Waters nativeID format, combined spectra -def: "Waters comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002649 -name: WIFF nativeID format, combined spectra -def: "WIFF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002650 -name: Bruker/Agilent YEP nativeID format, combined spectra -def: "Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002651 -name: Bruker BAF nativeID format, combined spectra -def: "Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002652 -name: Bruker FID nativeID format, combined spectra -def: "Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -comment: The nativeID must be the same as the source file ID. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002653 -name: multiple peak list nativeID format, combined spectra -def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002654 -name: single peak list nativeID format, combined spectra -def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -comment: The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002655 -name: scan number only nativeID format, combined spectra -def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002656 -name: spectrum identifier nativeID format, combined spectra -def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -comment: Used for conversion from mzData. The spectrum id attribute is referenced. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002657 -name: mzML unique identifier, combined spectra -def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -comment: A unique identifier of a spectrum stored in an mzML file. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002658 -name: identification parameter -def: "Identification parameter for the search engine run." [PSI:PI] -relationship: part_of MS:1001000 ! spectrum interpretation - -[Term] -id: MS:1002659 -name: UniProtKB text sequence format -def: "Text-based format used by UniProtKB for sequence entries." [PSI:PI] -xref: SWO:http://edamontology.org/format_2187 -is_a: MS:1001347 ! database file formats - -[Term] -id: MS:1002660 -name: UniProtKB XML sequence format -def: "XML-based format used by UniProtKB for sequence entries." [PSI:PI] -is_a: MS:1001347 ! database file formats - -[Term] -id: MS:1002661 -name: Morpheus -def: "Morpheus search engine." [PMID:23323968] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002662 -name: Morpheus:Morpheus score -def: "Morpheus score for PSMs." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002663 -name: Morpheus:summed Morpheus score -def: "Summed Morpheus score for protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002664 -name: interaction score derived from cross-linking -def: "Parent term for interaction scores derived from cross-linking." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002675 ! cross-linking result details -relationship: has_regexp MS:1002665 ! ([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})) -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002665 -name: regular expression for interaction scores derived from cross-linking -def: "([:digit:]+[.][a|b]:([:digit:]+|null):[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\}))." [PSI:PI] -is_a: MS:1002479 ! regular expression - -[Term] -id: MS:1002666 -name: impact II -def: "Bruker Daltonics' impact II." [PSI:MS] -is_a: MS:1001536 ! Bruker Daltonics micrOTOF series - -[Term] -id: MS:1002667 -name: impact HD -def: "Bruker Daltonics' impact HD." [PSI:MS] -is_a: MS:1001536 ! Bruker Daltonics micrOTOF series - -[Term] -id: MS:1002668 -name: frag: iTRAQ 4plex reporter ion -def: "Standard reporter ion for iTRAQ 4Plex. The value slot holds the integer mass of the iTRAQ 4Plex reporter ion, e.g. 114." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002307 ! fragmentation ion type -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002669 -name: frag: iTRAQ 8plex reporter ion -def: "Standard reporter ion for iTRAQ 8Plex. The value slot holds the integer mass of the iTRAQ 8Plex reporter ion, e.g. 113." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002307 ! fragmentation ion type -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002670 -name: frag: TMT reporter ion -def: "Standard reporter ion for TMT. The value slot holds the integer mass of the TMT reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127N." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002307 ! fragmentation ion type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002671 -name: frag: TMT ETD reporter ion -def: "Standard reporter ion for TMT with ETD fragmentation. The value slot holds the integer mass of the TMT ETD reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127C." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002307 ! fragmentation ion type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002672 -name: no modification threshold -def: "No statistical threshold for accepting or rejecting that a modification position." [PSI:PI] -is_a: MS:1002555 ! PTM localization score threshold - -[Term] -id: MS:1002673 -name: OpenXQuest -def: "Cross-Linking MS search engine." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1002674 -name: X500R QTOF -def: "SCIEX X500R QTOF, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1002675 -name: cross-linking result details -def: "This subsection describes terms which can describe details of cross-linking results." [PSI:PI] -relationship: part_of MS:1001000 ! spectrum interpretation - -[Term] -id: MS:1002676 -name: protein-pair-level global FDR -def: "Estimation of the global false discovery rate of proteins-pairs in cross-linking experiments." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002664 ! interaction score derived from cross-linking -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_regexp MS:1002665 ! ([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})) -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002677 -name: residue-pair-level global FDR -def: "Estimation of the global false discovery rate of residue-pairs in cross-linking experiments." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002664 ! interaction score derived from cross-linking -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_regexp MS:1002665 ! ([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})) -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002678 -name: supplemental beam-type collision-induced dissociation -def: "A supplemental collision-induced dissociation process that occurs in a beam-type collision cell in addition to another primary type of dissociation." [PSI:MS] -is_a: MS:1000422 ! beam-type collision-induced dissociation - -[Term] -id: MS:1002679 -name: supplemental collision-induced dissociation -def: "The dissociation of an ion after supplemental collisional excitation." [PSI:MS] -is_a: MS:1000133 ! collision-induced dissociation - -[Term] -id: MS:1002680 -name: supplemental collision energy -def: "Energy for an ion experiencing supplemental collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000510 ! precursor activation attribute -relationship: has_units UO:0000266 ! electronvolt -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002681 -name: OpenXQuest:combined score -def: "OpenXQuest's combined score for a cross-link spectrum match." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1001153 ! search engine specific score -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002682 -name: OpenXQuest:xcorr xlink -def: "OpenXQuest's cross-correlation of cross-linked ions subscore." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1001153 ! search engine specific score -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002683 -name: OpenXQuest:xcorr common -def: "OpenXQuest's cross-correlation of unlinked ions subscore." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1001153 ! search engine specific score -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002684 -name: OpenXQuest:match-odds -def: "OpenXQuest's match-odds subscore." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1001153 ! search engine specific score -relationship: has_order MS:1002108 ! higher score better -relationship: has_domain MS:1002306 ! value greater than zero -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002685 -name: OpenXQuest:intsum -def: "OpenXQuest's sum of matched peak intensity subscore." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1001153 ! search engine specific score -relationship: has_order MS:1002108 ! higher score better -relationship: has_domain MS:1002306 ! value greater than zero -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002686 -name: OpenXQuest:wTIC -def: "OpenXQuest's weighted percent of total ion current subscore." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1001153 ! search engine specific score -relationship: has_order MS:1002108 ! higher score better -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002687 -name: analysis attribute -def: "Attribute of an item in the result of mass spectrometry proteomics data analysis." [PSI:PI] -is_a: MS:1001405 ! spectrum identification result details - -[Term] -id: MS:1002688 -name: PTM localization attribute -def: "Statistic derived from a post-translational modification localization analysis." [PSI:PI] -is_a: MS:1002687 ! analysis attribute - -[Term] -id: MS:1002689 -name: PTM localization single result statistic -def: "Statistic for a single item derived from a post-translational modification localization analysis." [PSI:PI] -is_a: MS:1002688 ! PTM localization attribute - -[Term] -id: MS:1002690 -name: PTM localization result list statistic -def: "Statistic for all items derived from a post-translational modification localization analysis." [PSI:PI] -is_a: MS:1002688 ! PTM localization attribute - -[Term] -id: MS:1002691 -name: global FLR -def: "Global false localization rate for all localizations in a dataset." [PSI:PI] -is_a: MS:1002690 ! PTM localization result list statistic - -[Term] -id: MS:1002692 -name: local FLR at threshold -def: "Local false localization rate for the bottom item in list of localizations sorted from most to least confident." [PSI:PI] -is_a: MS:1002690 ! PTM localization result list statistic - -[Term] -id: MS:1002693 -name: identification attribute -def: "Attribute of an identification item in the result of mass spectrometry proteomics data analysis." [PSI:PI] -is_a: MS:1002687 ! analysis attribute - -[Term] -id: MS:1002694 -name: single identification result attribute -def: "Attribute of a single identification item (as opposed to a list) in the result of mass spectrometry proteomics data analysis." [PSI:PI] -is_a: MS:1002693 ! identification attribute - -[Term] -id: MS:1002695 -name: frag: isobaric label ion -def: "Fragment ion corresponding to an isobaric label artifact." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1002697 -name: secondary isotope peak -def: "Fragment ion is an isotopic peak other than that monoisotopic peak. This is used in conjuction with another ion type, such as frag: y ion." [PSI:PI] -is_a: MS:1002307 ! fragmentation ion type - -[Term] -id: MS:1002698 -name: protein cluster identification attribute -def: "An attribute of the protein cluster concept as used in mzIdentML." [PSI:PI] -is_a: MS:1002694 ! single identification result attribute - -[Term] -id: MS:1002699 -name: result list attribute -def: "General property of an entire result list." [PSI:PI] -is_a: MS:1002693 ! identification attribute - -[Term] -id: MS:1002700 -name: PSM-level result list attribute -def: "General property of the list of all PSMs." [PSI:PI] -is_a: MS:1002699 ! result list attribute - -[Term] -id: MS:1002701 -name: PSM-level result list statistic -def: "Statistic pertaining to the full list of all PSMs." [PSI:PI] -is_a: MS:1002700 ! PSM-level result list attribute - -[Term] -id: MS:1002702 -name: peptide sequence-level result list attribute -def: "General property of all peptide sequences in the list." [PSI:PI] -is_a: MS:1002699 ! result list attribute - -[Term] -id: MS:1002703 -name: peptide sequence-level result list statistic -def: "Statistic pertaining to all peptide sequences in the list." [PSI:PI] -is_a: MS:1002702 ! peptide sequence-level result list attribute - -[Term] -id: MS:1002704 -name: protein-level result list attribute -def: "Attribute of an entire protein list." [PSI:PI] -is_a: MS:1002699 ! result list attribute - -[Term] -id: MS:1002705 -name: protein-level result list statistic -def: "A statistical metric of an entire protein list." [PSI:PI] -is_a: MS:1002704 ! protein-level result list attribute - -[Term] -id: MS:1002706 -name: protein group-level result list statistic -def: "Attrbiute of an entire list of protein groups." [PSI:PI] -is_a: MS:1002405 ! protein group-level result list attribute - -[Term] -id: MS:1002707 -name: (?=[KR]) -def: "Regular expression for LysargiNase." [PSI:PI] -is_a: MS:1001180 ! Cleavage agent regular expression - -[Term] -id: MS:1002708 -name: LysargiNase -def: "Metalloproteinase found in Methanosarcina acetivorans that cleaves on the N-terminal side of lysine and arginine residues." [PMID:25419962] -synonym: "Tryp-N" EXACT [] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1002707 ! (?=[KR]) - -[Term] -id: MS:1002709 -name: compound data type -def: "A data type representing more than a single value." [] - -[Term] -id: MS:1002710 -name: list of type -def: "A data type defining a list of values of a single type." [] -is_a: MS:1002709 ! compound data type - -[Term] -id: MS:1002711 -name: list of strings -def: "A list of xsd:string." [] -is_a: MS:1002710 ! list of type -relationship: has_value_type xsd\:string - -[Term] -id: MS:1002712 -name: list of integers -def: "A list of xsd:integer." [] -is_a: MS:1002710 ! list of type -relationship: has_value_type xsd\:integer - -[Term] -id: MS:1002713 -name: list of floats -def: "A list of xsd:float." [] -is_a: MS:1002710 ! list of type -relationship: has_value_type xsd\:float - -[Term] -id: MS:1002719 -name: Pegasus BT -def: "LECO bench-top GC time-of-flight mass spectrometer." [PSI:PI] -is_a: MS:1001800 ! LECO instrument model - -[Term] -id: MS:1002720 -name: MSPathFinder -def: "PNNL top-down/bottom-up analysis software for identifying peptides and proteoforms in fragmentation mass spectra." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002721 -name: MSPathFinder:SpecEValue -def: "MSPathFinder spectral E-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002353 ! PSM-level e-value -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002722 -name: MSPathFinder:EValue -def: "MSPathFinder E-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002353 ! PSM-level e-value -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002723 -name: MSPathFinder:QValue -def: "MSPathFinder Q-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002354 ! PSM-level q-value -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002724 -name: MSPathFinder:PepQValue -def: "MSPathFinder peptide-level Q-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002725 -name: MSPathFinder:RawScore -def: "MSPathFinder raw score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002726 -name: SYNAPT G2-Si -def: "Waters Corporation SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1002727 -name: MALDI SYNAPT G2-Si -def: "Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1002728 -name: Vion IMS QTof -def: "Waters Corporation Vion IMS QTof orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1002729 -name: Xevo G2 XS Tof -def: "Waters Corporation Xevo G2 XS Tof orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1002730 -name: Xevo TQ-XS -def: "Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer." [PSI:PI] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1002731 -name: Xevo TQ-S micro -def: "Waters Corporation Xevo TQ-S micro triple quadrupole mass spectrometer." [PSI:PI] -is_a: MS:1000126 ! Waters instrument model - -[Term] -id: MS:1002732 -name: Orbitrap Fusion Lumos -def: "Thermo Scientific Orbitrap Fusion Lumos mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1002733 -name: peptide-level spectral count -def: "The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002734 -name: peptide ion-level spectral count -def: "The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002737 ! peptide-level quantification datatype -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: MS:1002735 -name: feature-level quantification datatype -def: "The data type of the value reported in a QuantLayer for a feature." [PSI:PI] -is_a: MS:1001805 ! quantification datatype - -[Term] -id: MS:1002736 -name: PSM-level quantification datatype -def: "The data type of the value reported in a QuantLayer for a PSM." [PSI:PI] -is_a: MS:1001805 ! quantification datatype - -[Term] -id: MS:1002737 -name: peptide-level quantification datatype -def: "The data type of the value reported in a QuantLayer for a peptide." [PSI:PI] -is_a: MS:1001805 ! quantification datatype - -[Term] -id: MS:1002738 -name: protein-level quantification datatype -def: "The data type of the value reported in a QuantLayer for a protein." [PSI:PI] -is_a: MS:1001805 ! quantification datatype - -[Term] -id: MS:1002739 -name: protein group-level quantification datatype -def: "The data type of the value reported in a QuantLayer for a protein group." [PSI:PI] -is_a: MS:1001805 ! quantification datatype - -[Term] -id: MS:1002740 -name: unmapped peptide -def: "Within the context of a proteogenomics approach, a peptide sequence that has not been mapped to a genomic location." [PSI:PI] -is_a: MS:1002636 ! proteogenomics attribute - -[Term] -id: MS:1002741 -name: unmapped protein -def: "Within the context of a proteogenomics approach, a protein sequence that has not been mapped to a genomic location." [PSI:PI] -is_a: MS:1002636 ! proteogenomics attribute - -[Term] -id: MS:1002742 -name: noise array -def: "A data array of noise values." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000523 "64-bit float" -is_a: MS:1000513 ! binary data array - -[Term] -id: MS:1002743 -name: sampled noise m/z array -def: "A data array of parallel, independent m/z values for a sampling of noise across a spectrum (typically much smaller than MS:1000514, the m/z array)." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000523 "64-bit float" -is_a: MS:1000513 ! binary data array -relationship: has_units MS:1000040 ! m/z - -[Term] -id: MS:1002744 -name: sampled noise intensity array -def: "A data array of intensity values for the amplitude of noise variation superposed on the baseline (MS:1002745) across a spectrum (for use with MS:1002743, sampled noise m/z array)." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000523 "64-bit float" -is_a: MS:1000513 ! binary data array -relationship: has_units MS:1000131 ! number of detector counts - -[Term] -id: MS:1002745 -name: sampled noise baseline array -def: "A data array of baseline intensity values (the intensity in the absence of analytes) for a sampling of noise across a spectrum (for use with MS:1002743, sampled noise m/z array)." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000523 "64-bit float" -is_a: MS:1000513 ! binary data array - -[Term] -id: MS:1002746 -name: MS-Numpress linear prediction compression followed by zlib compression -def: "Compression using MS-Numpress linear prediction compression and zlib." [https://github.com/ms-numpress/ms-numpress] -is_a: MS:1000572 ! binary data compression type - -[Term] -id: MS:1002747 -name: MS-Numpress positive integer compression followed by zlib compression -def: "Compression using MS-Numpress positive integer compression and zlib." [https://github.com/ms-numpress/ms-numpress] -is_a: MS:1000572 ! binary data compression type - -[Term] -id: MS:1002748 -name: MS-Numpress short logged float compression followed by zlib compression -def: "Compression using MS-Numpress short logged float compression and zlib." [https://github.com/ms-numpress/ms-numpress] -is_a: MS:1000572 ! binary data compression type - -[Term] -id: MS:1002749 -name: Mascot:IntegratedSpectralLibrarySearch -def: "Means that Mascot has integrated the search results of database and spectral library search into a single data set." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002750 -name: NIST MSPepSearch -def: "Search tool of the NIST (National Institute of Standards and Technology) for spectral library searches." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002751 -name: NIST MSP format -def: "MSP text format defined by the NIST." [PSI:PI] -is_a: MS:1001347 ! database file formats - -[Term] -id: MS:1002752 -name: database type spectral library -def: "Database containing spectra." [PSI:PI] -is_a: MS:1001073 ! database type amino acid - -[Term] -id: MS:1002753 -name: value between 0 and 1000 inclusive -def: "Value range for scores." [PSI:PI] -is_a: MS:1002304 ! domain range - -[Term] -id: MS:1002754 -name: MSPepSearch:score -def: "MSPepSearch score (0 for entirely dissimilar and 1000 for identical observed spectrum and library spectrum." [PSI:PI] -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_domain MS:1002753 ! value between 0 and 1000 inclusive - -[Term] -id: MS:1002755 -name: combined ms-ms + spectral library search -def: "A combined MS2 (with fragment ions) and spectral library search." [PSI:PI] -is_a: MS:1001080 ! search type - -[Term] -id: MS:1002756 -name: iodoTMT quantitation analysis -def: "Quantitation analysis using the Thermo Fisher sulfhydryl-reactive iodo tandem mass tag (iodoTMT) labelling workflow." [PSI:PI, PMID:24926564] -is_a: MS:1002009 ! isobaric label quantitation analysis - -[Term] -id: MS:1002757 -name: glyco-TMT quantitation analysis -def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive glyco-tandem mass tag (glyco-TMT) labelling workflow." [PSI:PI, PMID:22455665] -is_a: MS:1002009 ! isobaric label quantitation analysis - -[Term] -id: MS:1002758 -name: aminoxyTMT quantitation analysis -def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive aminoxy tandem mass tag (aminoxyTMT) labelling workflow." [PSI:PI, PMID:25337643] -is_a: MS:1002009 ! isobaric label quantitation analysis - -[Term] -id: MS:1002759 -name: hydrazideTMT quantitation analysis -def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive hydrazide tandem mass tag (hydrazide-TMT) labelling workflow." [PSI:PI, PMID:25337643] -is_a: MS:1002009 ! isobaric label quantitation analysis - -[Term] -id: MS:1002760 -name: iTRAQH quantitation analysis -def: "Quantification analysis using the carbonyl-reactive isobaric tags for relative and absolute quantification hydrazide (iTRAQH) labelling workflow." [PSI:PI, PMID:22926130] -is_a: MS:1002009 ! isobaric label quantitation analysis - -[Term] -id: MS:1002761 -name: DiART quantitation analysis -def: "Quantification analysis using the amine-reactive deuterium isobaric amine reactive tag (DiART) labelling workflow." [PSI:PI, PMID:20715779] -is_a: MS:1002009 ! isobaric label quantitation analysis - -[Term] -id: MS:1002762 -name: DiLeu quantitation analysis -def: "Quantification analysis using the amine-reactive dimethyl leucine (DiLeu) tag labelling workflow." [PSI:PI, PMID:20715779] -is_a: MS:1002009 ! isobaric label quantitation analysis - -[Term] -id: MS:1002763 -name: TMT reagent 127N -def: "The name of the sample labelled with the TMT reagent 127N." [PSI:PI] -is_a: MS:1002615 ! TMT reagent - -[Term] -id: MS:1002764 -name: TMT reagent 127C -def: "The name of the sample labelled with the TMT reagent 127C." [PSI:PI] -is_a: MS:1002615 ! TMT reagent - -[Term] -id: MS:1002765 -name: TMT reagent 128N -def: "The name of the sample labelled with the TMT reagent 128N." [PSI:PI] -is_a: MS:1002615 ! TMT reagent - -[Term] -id: MS:1002766 -name: TMT reagent 128C -def: "The name of the sample labelled with the TMT reagent 128C." [PSI:PI] -is_a: MS:1002615 ! TMT reagent - -[Term] -id: MS:1002767 -name: TMT reagent 129N -def: "The name of the sample labelled with the TMT reagent 129N." [PSI:PI] -is_a: MS:1002615 ! TMT reagent - -[Term] -id: MS:1002768 -name: TMT reagent 129C -def: "The name of the sample labelled with the TMT reagent 129C." [PSI:PI] -is_a: MS:1002615 ! TMT reagent - -[Term] -id: MS:1002769 -name: TMT reagent 130N -def: "The name of the sample labelled with the TMT reagent 130N." [PSI:PI] -is_a: MS:1002615 ! TMT reagent - -[Term] -id: MS:1002770 -name: TMT reagent 130C -def: "The name of the sample labelled with the TMT reagent 130C." [PSI:PI] -is_a: MS:1002615 ! TMT reagent - -[Term] -id: MS:1002771 -name: DiART reagent -def: "Deuterium isobaric amine reactive tag labeling reagent." [PSI:PI] -is_a: MS:1002602 ! sample label - -[Term] -id: MS:1002772 -name: DiART reagent 114 -def: "The name of the sample labelled with the DiART reagent 114." [PSI:PI] -is_a: MS:1002771 ! DiART reagent - -[Term] -id: MS:1002773 -name: DiART reagent 115 -def: "The name of the sample labelled with the DiART reagent 115." [PSI:PI] -is_a: MS:1002771 ! DiART reagent - -[Term] -id: MS:1002774 -name: DiART reagent 116 -def: "The name of the sample labelled with the DiART reagent 116." [PSI:PI] -is_a: MS:1002771 ! DiART reagent - -[Term] -id: MS:1002775 -name: DiART reagent 117 -def: "The name of the sample labelled with the DiART reagent 117." [PSI:PI] -is_a: MS:1002771 ! DiART reagent - -[Term] -id: MS:1002776 -name: DiART reagent 118 -def: "The name of the sample labelled with the DiART reagent 118." [PSI:PI] -is_a: MS:1002771 ! DiART reagent - -[Term] -id: MS:1002777 -name: DiART reagent 119 -def: "The name of the sample labelled with the DiART reagent 119." [PSI:PI] -is_a: MS:1002771 ! DiART reagent - -[Term] -id: MS:1002778 -name: DiLeu reagent -def: "Dimethyl leucine labeling reagent." [PSI:PI] -is_a: MS:1002602 ! sample label - -[Term] -id: MS:1002779 -name: DiLeu reagent 115 -def: "The name of the sample labelled with the DiLeu reagent 115." [PSI:PI] -is_a: MS:1002778 ! DiLeu reagent - -[Term] -id: MS:1002780 -name: DiLeu reagent 116 -def: "The name of the sample labelled with the DiLeu reagent 116." [PSI:PI] -is_a: MS:1002778 ! DiLeu reagent - -[Term] -id: MS:1002781 -name: DiLeu reagent 117 -def: "The name of the sample labelled with the DiLeu reagent 117." [PSI:PI] -is_a: MS:1002778 ! DiLeu reagent - -[Term] -id: MS:1002782 -name: DiLeu reagent 118 -def: "The name of the sample labelled with the DiLeu reagent 118." [PSI:PI] -is_a: MS:1002778 ! DiLeu reagent - -[Term] -id: MS:1002783 -name: 6550 iFunnel Q-TOF LC/MS -def: "The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002784 -name: 6550A iFunnel Q-TOF LC/MS -def: "The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002785 -name: 6520B Q-TOF LC/MS -def: "The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002786 -name: 6530A Q-TOF LC/MS -def: "The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002787 -name: 6530B Q-TOF LC/MS -def: "The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002788 -name: 6538 Q-TOF LC/MS -def: "The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002789 -name: 6540 Q-TOF LC/MS -def: "The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002790 -name: 6542 Q-TOF LC/MS -def: "The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002791 -name: 6545 Q-TOF LC/MS -def: "The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002792 -name: 6560 Q-TOF LC/MS -def: "The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002793 -name: 6570 Q-TOF LC/MS -def: "The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002794 -name: 6120B Quadrupole LC/MS -def: "The 6120B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002795 -name: 6150 Quadrupole LC/MS -def: "The 6150 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002796 -name: 6224 Time-of-Flight LC/MS -def: "The 6224 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002797 -name: 6230A Time-of-Flight LC/MS -def: "The 6230A Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002798 -name: 6230B Time-of-Flight LC/MS -def: "The 6230B Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002799 -name: 6430 Triple Quadrupole LC/MS -def: "The 6430 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002800 -name: 6495A Triple Quadrupole LC/MS -def: "The 6495A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002801 -name: 6495B Triple Quadrupole LC/MS -def: "The 6495B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002802 -name: 7000A Triple Quadrupole GC/MS -def: "The 7000A Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002803 -name: 7000B Triple Quadrupole GC/MS -def: "The 7000B Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002804 -name: 7800 Quadrupole ICP-MS -def: "The 7800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002805 -name: 8800 Triple Quadrupole ICP-MS -def: "The 8800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer." [PSI:MS] -is_a: MS:1000490 ! Agilent instrument model - -[Term] -id: MS:1002806 -name: ion -def: "Molecular entity having a net positive or negative electric charge." [PSI:MS] -is_a: MS:1000881 ! molecular entity - -[Term] -id: MS:1002807 -name: positive mode adduct ion -def: "Adduct ion with positive ionization." [PSI:MS] -is_a: MS:1000353 ! adduct ion - -[Term] -id: MS:1002808 -name: negative mode adduct ion -def: "Adduct ion with negative ionization." [PSI:MS] -is_a: MS:1000353 ! adduct ion - -[Term] -id: MS:1002809 -name: adduct ion attribute -def: "Nonphysical characteristic attributed to an adduct ion." [PSI:MS] -relationship: part_of MS:1000353 ! adduct ion - -[Term] -id: MS:1002810 -name: adduct ion X m/z -def: "Theoretical m/z of the X component in the adduct M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1003056 ! adduct ion property -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002811 -name: adduct ion isotope -def: "Isotope of the matrix molecule M of an adduct formation." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1003056 ! adduct ion property -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002812 -name: Regular expression for adduct ion formula -def: "(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-])." [PSI:PI] -is_a: MS:1002479 ! regular expression - -[Term] -id: MS:1002813 -name: adduct ion formula -def: "Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002809 ! adduct ion attribute -relationship: has_regexp MS:1002812 ! (\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-]) -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002814 -name: volt-second per square centimeter -def: "An electrical mobility unit that equals the speed [cm/s] an ion reaches when pulled through a gas by a Voltage[V] over a certain distance [cm]." [PSI:PI] -synonym: "Vs/cm^2" EXACT [] -is_a: UO:0000000 ! unit - -[Term] -id: MS:1002815 -name: inverse reduced ion mobility -def: "Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000455 ! ion selection attribute -is_a: MS:1002892 ! ion mobility attribute -relationship: has_units MS:1002814 ! volt-second per square centimeter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002816 -name: mean ion mobility array -def: "Array of population mean ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002893 ! ion mobility array -relationship: has_units UO:0000028 ! millisecond -relationship: has_units UO:0000010 ! second -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002817 -name: Bruker TDF format -def: "Bruker TDF raw file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1002818 -name: Bruker TDF nativeID format -def: "Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS] -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1002819 -name: Bruker TDF nativeID format, combined spectra -def: "Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002646 ! native spectrum identifier format, combined spectra -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002820 -name: M+H ion -def: "Adduct formed by protonation of a matrix molecule M, i.e. the addition of a matrix molecule M plus a proton." [PSI:MS] -property_value: ionMass: "M + 1.007276" xsd:string -is_a: MS:1002807 ! positive mode adduct ion - -[Term] -id: MS:1002821 -name: M-H ion -def: "Adduct formed by deprotonation of a matrix molecule M, i.e. the removal of a proton from a matrix molecule M." [PSI:MS] -property_value: ionMass: "M - 1.007276" xsd:string -is_a: MS:1002808 ! negative mode adduct ion - -[Term] -id: MS:1002822 -name: OpenMS file format -def: "File format developed by the OpenMS team." [PMID:27575624] -is_a: MS:1001459 ! file format - -[Term] -id: MS:1002823 -name: idXML -def: "OpenMS intermediate identification format." [PSI:PI] -is_a: MS:1002822 ! OpenMS file format - -[Term] -id: MS:1002824 -name: featureXML -def: "OpenMS feature file format." [PSI:PI] -is_a: MS:1002822 ! OpenMS file format - -[Term] -id: MS:1002825 -name: consensusXML -def: "OpenMS consensus map format." [PSI:PI] -is_a: MS:1002822 ! OpenMS file format - -[Term] -id: MS:1002826 -name: MetaMorpheus -def: "MetaMorpheus search engine." [https://github.com/smith-chem-wisc/MetaMorpheus] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002827 -name: MetaMorpheus:score -def: "MetaMorpheus score for PSMs." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002828 -name: MetaMorpheus:protein score -def: "MetaMorpheus score for protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002829 -name: XCMS:into -def: "Feature intensity produced by XCMS findPeaks() from integrated peak intensity." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002830 -name: XCMS:intf -def: "Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002831 -name: XCMS:maxo -def: "Feature intensity produced by XCMS findPeaks() from maximum peak intensity." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002832 -name: XCMS:area -def: "Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002735 ! feature-level quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002833 -name: alternating polarity mode -def: "Polarities of the scans of a run are alternating, i.e. both positive and negative mode scans are acquired." [PSI:PI] -is_a: MS:1000857 ! run attribute - -[Term] -id: MS:1002834 -name: ProteomeDiscoverer:Delta Score -def: "The Delta Score reported by Proteome Discoverer version 2." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002835 -name: LTQ Orbitrap Classic -def: "Thermo Fisher Scientific LTQ Orbitrap Classic." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1002836 -name: iProX dataset identifier -def: "Dataset identifier issued by the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002837 -name: iProX dataset URI -def: "URI that allows the access to one dataset in the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term - -[Term] -id: MS:1002838 -name: mzMLb format -def: "mzMLb file format, mzML encapsulated within HDF5." [PSI:PI, https://github.com/biospi/mzmlb] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1002839 -name: Conversion to mzMLb -def: "Conversion of a file format to Proteomics Standards Initiative mzMLb file format." [PSI:PI] -is_a: MS:1000530 ! file format conversion - -[Term] -id: MS:1002840 -name: external reference data -def: "Data belonging to an external reference." [PSI:MS] -relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies - -[Term] -id: MS:1002841 -name: external HDF5 dataset -def: "The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the section of the BinaryDataArray." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002840 ! external reference data -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002842 -name: external offset -def: "The position in the external data where the array begins." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -relationship: has_units UO:0000189 ! Count -is_a: MS:1002840 ! external reference data -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1002843 -name: external array length -def: "Describes how many fields an array contains." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -relationship: has_units UO:0000189 ! Count -is_a: MS:1002840 ! external reference data -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1002844 -name: Experiment additional parameter -def: "Root node for terms relating to the description of an Experiment in relation to the PRIDE-XML element ExperimentCollection/Experiment/additional/cvParam." [PSI:PI] -is_a: MS:1001458 ! spectrum generation information - -[Term] -id: MS:1002845 -name: Associated file URI -def: "URI of one external file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002844 ! Experiment additional parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002846 -name: Associated raw file URI -def: "URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002845 ! Associated file URI -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002847 -name: ProteomeCentral dataset URI -def: "URI associated to one PX submission in ProteomeCentral." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002844 ! Experiment additional parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002848 -name: Result file URI -def: "URI of one file labeled as 'Result', associated to one PX submission." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002845 ! Associated file URI -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002849 -name: Search engine output file URI -def: "URI of one search engine output file associated to one PX submission." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002845 ! Associated file URI -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002850 -name: Peak list file URI -def: "URI of one of one search engine output file associated to one PX submission." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002845 ! Associated file URI -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002851 -name: Other type file URI -def: "URI of one file labeled as 'Other', associated to one PX submission." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002845 ! Associated file URI -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002852 -name: Dataset FTP location -def: "FTP location of one entire PX data set." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002844 ! Experiment additional parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002853 -name: Dataset with no associated published manuscript -def: "A dataset which does not have an associated published manuscript." [PSI:PI] -is_a: MS:1002844 ! Experiment additional parameter - -[Term] -id: MS:1002854 -name: Peer-reviewed dataset -def: "Dataset has been peer-reviewed somehow." [PSI:PI] -is_a: MS:1002844 ! Experiment additional parameter - -[Term] -id: MS:1002855 -name: Non peer-reviewed dataset -def: "Dataset that has not been peer-reviewed by any means." [PSI:PI] -is_a: MS:1002844 ! Experiment additional parameter - -[Term] -id: MS:1002856 -name: Supported dataset by repository -def: "Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. This is usually called a complete submission." [PSI:PI] -is_a: MS:1002844 ! Experiment additional parameter - -[Term] -id: MS:1002857 -name: Unsupported dataset by repository -def: "Dataset for which the identifications and/or spectra/traces are in formats that cannot be parsed by the hosting data repository and thus internal references between identifications and spectra/traces are not browsable at the repository. This is usually called a partial submission." [PSI:PI] -is_a: MS:1002844 ! Experiment additional parameter - -[Term] -id: MS:1002858 -name: Dataset with its publication pending -def: "A dataset which has an associated manuscript pending for publication." [PSI:PI] -is_a: MS:1002844 ! Experiment additional parameter - -[Term] -id: MS:1002859 -name: Additional associated raw file URI -def: "Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002845 ! Associated file URI -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002860 -name: Gel image file URI -def: "URI of one gel image file associated to one PX submission." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002845 ! Associated file URI -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002861 -name: Reprocessed complete dataset -def: "All the raw files included in the original dataset (or group of original datasets) have been reanalysed." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002844 ! Experiment additional parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002862 -name: Reprocessed subset dataset -def: "A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002844 ! Experiment additional parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002863 -name: Data derived from previous dataset -def: "One dataset is a reanalysis of previously published data." [PSI:PI] -is_a: MS:1002844 ! Experiment additional parameter - -[Term] -id: MS:1002864 -name: No PTMs are included in the dataset -def: "No post-translational-modifications are been included in the identified peptides of one dataset." [PSI:PI] -is_a: MS:1002844 ! Experiment additional parameter - -[Term] -id: MS:1002865 -name: Accepted manuscript -def: "A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet." [PSI:PI] -is_a: MS:1002844 ! Experiment additional parameter - -[Term] -id: MS:1002866 -name: Reference -def: "Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002844 ! Experiment additional parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002867 -name: Experimental information has been refined since this experiment was originally made publicly available -def: "This means that the experimental information available has been improved, for instance precursor charges were added." [PSI:PI] -is_a: MS:1002844 ! Experiment additional parameter - -[Term] -id: MS:1002868 -name: Original data -def: "One dataset is not a reanalysis of previously published data." [PSI:PI] -is_a: MS:1002844 ! Experiment additional parameter - -[Term] -id: MS:1002869 -name: mzR -def: "Bioconductor package mzR for reading and writing mass spectrometry data files." [PSI:PI] -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002870 -name: MSnbase -def: "Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data." [PMID:22113085] -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002871 -name: CAMERA -def: "Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments." [PMID:22111785] -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002872 -name: Panorama Public dataset identifier -def: "Dataset identifier issued by the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002873 -name: Panorama Public dataset URI -def: "URI that allows the access to one dataset in the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:anyURI ! The allowed value-type for this CV term - -[Term] -id: MS:1002874 -name: TSQ Altis -def: "Thermo Scientific TSQ Altis Triple Quadrupole MS." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1002875 -name: TSQ Quantis -def: "Thermo Scientific TSQ Quantis Triple Quadrupole MS." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1002876 -name: TSQ 9000 -def: "Thermo Scientific TSQ 9000 Triple Quadrupole MS." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1002877 -name: Q Exactive HF-X -def: "Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1002878 -name: small molecule analysis software -def: "Software for the analysis of small molecules." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002879 -name: Progenesis QI -def: "Metabolomics analysis software for LC-MS data from Nonlinear Dynamics." [PSI:PI] -is_a: MS:1002878 ! small molecule analysis software - -[Term] -id: MS:1002880 -name: Compound Discoverer -def: "Metabolomics analysis software from Thermo Fisher Scientific." [PSI:PI] -is_a: MS:1002878 ! small molecule analysis software - -[Term] -id: MS:1002881 -name: MyCompoundID -def: "Metabolite identification tool MyCompoundID." [PSI:PI, PMID:23373753] -is_a: MS:1002878 ! small molecule analysis software - -[Term] -id: MS:1002882 -name: study variable average function -def: "Function used to calculate the study variable quantification value." [PSI:PI] -is_a: MS:1001184 ! search statistics - -[Term] -id: MS:1002883 -name: median -def: "Median function." [PSI:PI] -is_a: MS:1002882 ! study variable average function - -[Term] -id: MS:1002884 -name: study variable variation function -def: "Function used to calculate the study variable quantification variation value." [PSI:PI] -is_a: MS:1001184 ! search statistics - -[Term] -id: MS:1002885 -name: standard error -def: "Standard error function." [PSI:PI] -is_a: MS:1002884 ! study variable variation function - -[Term] -id: MS:1002886 -name: small molecule quantification datatype -def: "The value reported in a small molecule quantification." [PSI:PI] -is_a: MS:1001805 ! quantification datatype - -[Term] -id: MS:1002887 -name: Progenesis QI normalised abundance -def: "The normalised abundance produced by Progenesis QI LC-MS." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002886 ! small molecule quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002888 -name: small molecule confidence measure -def: "The confidence score produced by a small molecule analysis software." [PSI:PI] -is_a: MS:1002694 ! single identification result attribute - -[Term] -id: MS:1002889 -name: Progenesis MetaScope score -def: "The confidence score produced by Progenesis QI." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002888 ! small molecule confidence measure -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002890 -name: fragmentation score -def: "The fragmentation confidence score." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002888 ! small molecule confidence measure -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002891 -name: isotopic fit score -def: "The isotopic fit confidence score." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002888 ! small molecule confidence measure -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1002892 -name: ion mobility attribute -def: "An attribute describing ion mobility searches." [PSI:PI] -is_a: MS:1000503 ! scan attribute -is_a: MS:1002345 ! PSM-level attribute - -[Term] -id: MS:1002893 -name: ion mobility array -def: "Abstract array of ion mobility data values. A more specific child term concept should be specified in data files to make precise the nature of the data being provided." [PSI:PI] -is_a: MS:1000513 ! binary data array - -[Term] -id: MS:1002894 -name: InChIKey -def: "Unique chemical structure identifier for chemical compounds." [PMID:273343401] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001405 ! spectrum identification result details -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002895 -name: small molecule identification attribute -def: "Compound identification information." [PSI:PI] -is_a: MS:1002694 ! single identification result attribute - -[Term] -id: MS:1002896 -name: compound identification confidence level -def: "Confidence level for annotation of identified compounds as defined by the Metabolomics Standards Initiative (MSI). The value slot can have the values 'Level 0' until 'Level 4'." [PMID:29748461] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002895 ! small molecule identification attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002897 -name: isotopomer peak -def: "OBSOLETE Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'." [PSI:PI] -comment: This term was obsoleted because it was replaced by the more exact terms MS:1002956 'isotopic ion MS peak', MS:1002957 'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead. -xref: value-type:xsd:string "The allowed value-type for this CV term." -is_a: MS:1000231 ! peak -is_obsolete: true -relationship: has_value_type xsd:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002898 -name: Shimadzu Biotech QTOF nativeID format -def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:PI] -is_a: MS:1000767 ! native spectrum identifier format - -[Term] -id: MS:1002899 -name: msalign format -def: "msalign file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1002900 -name: feature format -def: "TopFD feature file format." [PSI:MS] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1002901 -name: TopPIC -def: "TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization." [PMID:27423895, http://proteomics.informatics.iupui.edu/software/toppic/index.html] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002902 -name: TopFD -def: "Top-down mass spectral feature detection." [http://proteomics.informatics.iupui.edu/software/toppic/index.html] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002903 -name: TopMG -def: "A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra." [PMID:28453668, http://proteomics.informatics.iupui.edu/software/topmg/index.html] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002904 -name: proteoform-level identification attribute -def: "Proteoform level information." [PSI:PI] -is_a: MS:1002694 ! single identification result attribute - -[Term] -id: MS:1002905 -name: proteoform-level identification statistic -def: "Identification confidence metric for a proteoform." [PSI:PI] -is_a: MS:1002904 ! proteoform-level identification attribute - -[Term] -id: MS:1002906 -name: search engine specific score for proteoforms -def: "Search engine specific proteoform scores." [PSI:PI] -is_a: MS:1002905 ! proteoform-level identification statistic - -[Term] -id: MS:1002907 -name: proteoform-level global FDR -def: "Estimation of the global false discovery rate of proteoforms." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002905 ! proteoform-level identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002908 -name: proteoform-level local FDR -def: "Estimation of the local false discovery rate of proteoforms." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002905 ! proteoform-level identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002909 -name: proteoform-level statistical threshold -def: "Estimated statistical threshold at proteoform-level." [PSI:PI] -is_a: MS:1002573 ! spectrum identification statistical threshold - -[Term] -id: MS:1002910 -name: proteoform-level global FDR threshold -def: "Threshold for the global false discovery rate of proteoforms." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002909 ! proteoform-level statistical threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002911 -name: proteoform-level local FDR threshold -def: "Threshold for the local false discovery rate of proteoforms." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002909 ! proteoform-level statistical threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002912 -name: TopPIC input parameter -def: "Search engine input parameters specific to TopPIC." [PSI:PI] -is_a: MS:1001302 ! search engine specific input parameter - -[Term] -id: MS:1002913 -name: TopPIC:fixed modification -def: "Fixed modifications for TopPIC searching." [PSI:PI] -is_a: MS:1002912 ! TopPIC input parameter - -[Term] -id: MS:1002914 -name: TopPIC:N-term form -def: "N-terminal forms of proteins allowed in TopPIC searching." [PSI:PI] -is_a: MS:1002912 ! TopPIC input parameter - -[Term] -id: MS:1002915 -name: TopPIC:error tolerance -def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1002916 -name: TopPIC:max shift -def: "Maximum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1002917 -name: TopPIC:min shift -def: "Minimum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1002918 -name: TopPIC:shift num -def: "Maximum number of unexpected modifications in a proteoform spectrum match." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1002919 -name: TopPIC:spectral cutoff type -def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002920 -name: TopPIC:spectral cutoff value -def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002921 -name: TopPIC:proteoform-level cutoff type -def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002922 -name: TopPIC:proteoform-level cutoff value -def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002923 -name: TopPIC:generating function -def: "P-value and E-value estimation using generating function." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002924 -name: TopPIC:combined spectrum number -def: "Number of combined spectra." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1002925 -name: TopPIC:mod file -def: "The text file containing the information of common PTMs." [PSI:PI] -is_a: MS:1002912 ! TopPIC input parameter - -[Term] -id: MS:1002926 -name: TopPIC:thread number -def: "Number of threads used in TopPIC." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1002927 -name: TopPIC:use TopFD feature -def: "Proteoform identification using TopFD feature file." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002912 ! TopPIC input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002928 -name: TopPIC:spectral E-value -def: "TopPIC spectrum-level E-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1002353 ! PSM-level e-value -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002929 -name: TopPIC:spectral FDR -def: "TopPIC spectrum-level FDR." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1002351 ! PSM-level local FDR -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002930 -name: TopPIC:proteoform-level FDR -def: "TopPIC proteoform-level FDR." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002908 ! proteoform-level local FDR -is_a: MS:1002906 ! search engine specific score for proteoforms -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002931 -name: TopPIC:spectral p-value -def: "TopPIC spectrum-level p-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1002352 ! PSM-level p-value -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002932 -name: TopPIC:MIScore -def: "Modification identification score." [PMID:27291504] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002933 -name: TopPIC:MIScore threshold -def: "TopPIC:MIScore threshold." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002555 ! PTM localization score threshold -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002934 -name: TopMG input parameter -def: "Search engine input parameters specific to TopMG." [PSI:PI] -is_a: MS:1001302 ! search engine specific input parameter - -[Term] -id: MS:1002935 -name: TopMG:fixed modification -def: "Fixed modifications for TopMG searching." [PSI:PI] -is_a: MS:1002934 ! TopMG input parameter - -[Term] -id: MS:1002936 -name: TopMG:N-term form -def: "N-terminal forms of proteins allowed in TopMG searching." [PSI:PI] -is_a: MS:1002934 ! TopMG input parameter - -[Term] -id: MS:1002937 -name: TopMG:error tolerance -def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1002938 -name: TopMG:max shift -def: "Maximum value of the mass shift (in Dalton)." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1002939 -name: TopMG:spectral cutoff type -def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002940 -name: TopMG:spectral cutoff value -def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002941 -name: TopMG:proteoform-level cutoff type -def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002942 -name: TopMG:proteoform-level cutoff value -def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002943 -name: TopMG:mod file -def: "The text file containing the information of common PTMs." [PSI:PI] -is_a: MS:1002934 ! TopMG input parameter - -[Term] -id: MS:1002944 -name: TopMG:thread number -def: "Number of threads used in TopMG." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1002945 -name: TopMG:use TopFD feature -def: "Proteoform identification using TopFD feature file." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002946 -name: TopMG:proteoform graph gap size -def: "Gap size in constructing proteoform graph." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1002947 -name: TopMG:variable PTM number -def: "Maximum number of variable PTMs." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1002948 -name: TopMG:variable PTM number in proteoform graph gap -def: "Maximum number of variable PTMs in a proteoform graph gap." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: MS:1002949 -name: TopMG:use ASF-DIAGONAL -def: "Protein filtering using ASF-DIAGONAL method." [PMID:29327814] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1002934 ! TopMG input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1002950 -name: TopMG:spectral E-value -def: "TopMG spectrum-level E-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002353 ! PSM-level e-value -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002951 -name: TopMG:spectral FDR -def: "TopMG spectrum-level FDR." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002351 ! PSM-level local FDR -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002952 -name: TopMG:proteoform-level FDR -def: "TopMG proteoform-level FDR." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002908 ! proteoform-level local FDR -is_a: MS:1002906 ! search engine specific score for proteoforms -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002953 -name: TopMG:spectral p-value -def: "TopMG spectrum-level p-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002352 ! PSM-level p-value -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002954 -name: collisional cross sectional area -def: "Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1000861 ! molecular entity property -relationship: has_units UO:0000324 ! square angstrom -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002955 -name: hr-ms compound identification confidence level -def: "Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'." [PMID:24476540] -xref: value-type:xsd:string "The allowed value-type for this CV term." -is_a: MS:1002895 ! small molecule identification attribute -relationship: has_value_type xsd:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002956 -name: isotopic ion MS peak -def: "A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000231 ! peak -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002957 -name: isotopomer MS peak -def: "The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002956 ! isotopic ion MS peak -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002958 -name: isotopologue MS peak -def: "The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002956 ! isotopic ion MS peak -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002959 -name: isomer -def: "One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae." [https://goldbook.iupac.org/html/I/I03289.html] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000859 ! molecule -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002960 -name: isotopomer -def: "An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms." [https://goldbook.iupac.org/html/I/I03352.html] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002959 ! isomer -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002961 -name: isotopologue -def: "A molecular entity that differs only in isotopic composition (number of isotopic substitutions)." [https://goldbook.iupac.org/html/I/I03351.html] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002959 ! isomer -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1002962 -name: mean -def: "The arithmetic mean." [PSI:PI] -is_a: MS:1002882 ! study variable average function - -[Term] -id: MS:1002963 -name: variation coefficient -def: "The coefficient of variation." [PSI:PI] -is_a: MS:1002884 ! study variable variation function - -[Term] -id: MS:1002964 -name: lipidomics analysis software -def: "Lipidomics analysis software." [PSI:PI] -is_a: MS:1002878 ! small molecule analysis software - -[Term] -id: MS:1002965 -name: Lipid Data Analyzer -def: "Lipid Data Analyzer software for lipid quantification." [PMID:29058722] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002966 -name: chrom format -def: "The Lipid Data Analyzer native chrom format." [PSI:PI] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1002967 -name: LipidHunter -def: "Software for identification of phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets." [PMID:28753264] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002968 -name: LipidXplorer -def: "Software for consensual cross-platform lipidomics." [PMID:22272252] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002969 -name: LipidMatch -def: "An automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data." [PMID:28693421] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002970 -name: Greazy -def: "Open-source software for automated phospholipid tandem mass spectrometry identification." [PMID:27186799] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002971 -name: LipidBlast -def: "LC-MS-based lipidomics and automated identification of lipids using the LipidBlast in-silico MS/MS library." [PMID:28660581] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002972 -name: Lipid-Pro -def: "A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms." [PMID:25433698] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002973 -name: LipidFinder -def: "A computational workflow for the discovery of lipids for the identification of eicosanoid-phosphoinositides in platelets." [PMID:28405621] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002974 -name: LipiDex -def: "An integrated software package for high-confidence lipid identification." [PMID:29705063] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002975 -name: LIQUID -def: "An-open source software for identifying lipids in LC-MS/MS-based lipidomics data." [PMID:28158427] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002976 -name: ALEX -def: "Analysis of lipid experiments, a calculator for m/z values of intact lipid molecules (MS1)." [PMID:24244551] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002977 -name: ALEX123 -def: "Analysis of lipid experiments 123, a calculator with m/z values of intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 level." [PMID:29786091] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002978 -name: LIMSA -def: "Software tool for the quantitative analysis of mass spectrometric lipidome data." [PMID:17165823] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002979 -name: LOBSTAHS -def: "Adduct-Based lipidomics software for the discovery and identification of oxidative stress biomarkers." [PMID:27322848] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002980 -name: LipidQA -def: "Lipid qualitative/quantitative analysis software for identification and quantitation of complex lipid molecular species." [PMID:17720531] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002981 -name: Proline -def: "The Proline software suite for mass spectrometry based proteomics." [http://www.profiproteomics.fr/proline/] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002982 -name: PepNovo -def: "PepNovo tool for de novo peptide sequencing." [PMID:15858974] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002983 -name: pNovo -def: "pNovo tool for de novo peptide sequencing and identification using HCD spectra." [PMID:20329752] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002984 -name: Novor -def: "Novor real-time peptide de novo sequencing software tool." [PMID:26122521] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002985 -name: in-gel digestion -def: "Digestion of proteins separated by gel electrophoresis for mass spectrometric characterization of proteins and proteomes." [PSI:PI] -is_a: MS:1000831 ! sample preparation - -[Term] -id: MS:1002986 -name: in-solution digestion -def: "Digestion of proteins in solution for mass spectrometric characterization of proteins and proteomes." [PSI:PI] -is_a: MS:1000831 ! sample preparation - -[Term] -id: MS:1002987 -name: IdentiPy -def: "IdentiPy." [PMID:29682971, https://bitbucket.org/levitsky/identipy] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1002988 -name: IdentiPy:RHNS -def: "The IdentiPy result 'RHNS'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001153 ! search engine specific score -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002989 -name: IdentiPy:hyperscore -def: "The IdentiPy result 'hyperscore'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001153 ! search engine specific score -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002990 -name: ms_deisotope -def: "ms_deisotope, a library for deisotoping and charge state deconvolution of mass spectra." [https://github.com/mobiusklein/ms_deisotope] -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1002991 -name: python-psims -def: "python-psims, a library for generating mzML and mzIdentML." [https://github.com/mobiusklein/psims] -is_a: MS:1002333 ! conversion software - -[Term] -id: MS:1002995 -name: Andromeda:PEP -def: "Posterior error probability of the best identified peptide of the Andromeda search engine." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1002996 -name: Andromeda:apl file format -def: "Peak list file format of the Andromeda search engine." [PSI:PI] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1002997 -name: ProteomeXchange dataset identifier reanalysis number -def: "Index number of a reanalysis within a ProteomeXchange reprocessed dataset identifier container (RPXD)." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1002998 -name: LCMS-9030 -def: "Shimadzu Scientific Instruments LCMS-9030 Q-TOF MS." [PSI:MS] -is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model - -[Term] -id: MS:1002999 -name: LCMS-8060 -def: "Shimadzu Scientific Instruments LCMS-8060 MS." [PSI:MS] -is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model - -[Term] -id: MS:1003000 -name: LCMS-8050 -def: "Shimadzu Scientific Instruments LCMS-8050 MS." [PSI:MS] -is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model - -[Term] -id: MS:1003001 -name: LCMS-8045 -def: "Shimadzu Scientific Instruments LCMS-8045 MS." [PSI:MS] -is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model - -[Term] -id: MS:1003002 -name: LCMS-8040 -def: "Shimadzu Scientific Instruments LCMS-8040 MS." [PSI:MS] -is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model - -[Term] -id: MS:1003003 -name: LCMS-2020 -def: "Shimadzu Scientific Instruments LCMS-2020." [PSI:MS] -is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model - -[Term] -id: MS:1003004 -name: maXis II -def: "Bruker Daltonics' maXis II." [PSI:MS] -is_a: MS:1001547 ! Bruker Daltonics maXis series - -[Term] -id: MS:1003005 -name: timsTOF Pro -def: "Bruker Daltonics' timsTOF Pro." [PSI:MS] -is_a: MS:1003123 ! Bruker Daltonics timsTOF series - -[Term] -id: MS:1003006 -name: mean inverse reduced ion mobility array -def: "Array of population mean ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002893 ! ion mobility array -relationship: has_units MS:1002814 ! volt-second per square centimeter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1003007 -name: raw ion mobility array -def: "Array of raw ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002893 ! ion mobility array -relationship: has_units UO:0000028 ! millisecond -relationship: has_units UO:0000010 ! second -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1003008 -name: raw inverse reduced ion mobility array -def: "Array of raw ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002893 ! ion mobility array -relationship: has_units MS:1002814 ! volt-second per square centimeter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1003009 -name: Shimadzu Biotech LCD format -def: "Shimadzu Biotech LCD file format." [PSI:PI] -is_a: MS:1000560 ! mass spectrometer file format - -[Term] -id: MS:1003010 -name: LPPtiger -def: "Software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets." [PMID:29123162] -is_a: MS:1002964 ! lipidomics analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1003011 -name: pFind -def: "Sequence-tag-based search engine pFind." [PMID:30295672] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1003012 -name: KSDP score -def: "Kernel mass spectral dot product scoring function." [PMID:15044235] -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better - -[Term] -id: MS:1003013 -name: i3tms -def: "i3-tms search engine and data-analysis software." [PSI:PI] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1003014 -name: MSFragger -def: "A database search-based peptide identification tool." [PMID:28394336] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1003015 -name: razor peptide -def: "Peptide that is shared between protein groups and assigned to the protein group with the largest number of identified peptides." [PSI:MS] -is_a: MS:1000860 ! peptide - -[Term] -id: MS:1003016 -name: ProteinProphet:peptide weight -def: "Fraction of peptide evidence attributable to a protein or a set of indistinguishable proteins." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002490 ! peptide-level scoring -is_a: MS:1001153 ! search engine specific score -relationship: has_order MS:1002108 ! higher score better -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1003017 -name: ProteinProphet:peptide group weight -def: "Fraction of peptide evidence attributable to a group of proteins." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002490 ! peptide-level scoring -is_a: MS:1001153 ! search engine specific score -relationship: has_order MS:1002108 ! higher score better -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1003018 -name: Philosopher -def: "General proteomics processing toolkit for shotgun proteomics." [https://philosopher.nesvilab.org/] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1003019 -name: pressure chromatogram -def: "Representation of chromatographic pressure versus time." [PSI:MS] -is_a: MS:1000626 ! chromatogram type - -[Term] -id: MS:1003020 -name: flow rate chromatogram -def: "Representation of the chromatographic flow rate versus time." [PSI:MS] -is_a: MS:1000626 ! chromatogram type - -[Term] -id: MS:1003021 -name: Fixed modification -def: "Post-translational modification which is assumed to be present at each instance of a residue type." [PSI:PI] -is_a: MS:1001055 ! modification parameters -is_a: MS:1003026 ! named element in mzIdentML - -[Term] -id: MS:1003022 -name: Variable modification -def: "Post-translational modification which may or may not be present at a residue type." [PSI:PI] -is_a: MS:1001055 ! modification parameters -is_a: MS:1003026 ! named element in mzIdentML - -[Term] -id: MS:1003023 -name: OpenPepXL -def: "Cross-Linking MS search engine." [PSI:PI] -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1003024 -name: OpenPepXL:score -def: "The OpenPepXL score for a cross-link spectrum match." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -is_a: MS:1001153 ! search engine specific score -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003025 -name: named element -def: "A named element that is an attribute in a proteomics standards file." [PSI:PI] -relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies - -[Term] -id: MS:1003026 -name: named element in mzIdentML -def: "A named element that is an attribute in a mzIdentML file." [PSI:PI] -is_a: MS:1003025 ! named element - -[Term] -id: MS:1003027 -name: named element in mzML -def: "A named element that is an attribute in a mzML file." [PSI:PI] -is_a: MS:1003025 ! named element - -[Term] -id: MS:1003028 -name: Orbitrap Exploris 480 -def: "Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1003029 -name: Orbitrap Eclipse -def: "Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1003030 -name: Mascot:MinNumSigUniqueSeqs -def: "Minimum number of significant unique sequences required in a protein hit. The setting is only relevant if the protein grouping strategy is 'family clustering'." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." -is_a: MS:1002095 ! Mascot input parameter -relationship: has_value_type xsd\:nonNegativeInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1003031 -name: CPTAC accession number -def: "Main identifier of a CPTAC dataset." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1003032 -name: compound identification confidence code in MS-DIAL -def: "The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program." [PMID:25938372, http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002895 ! small molecule identification attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1003033 -name: molecular entity attribute -def: "Non-inherent characteristic attributed to a molecular entity." [PSI:PI] -relationship: part_of MS:1000881 ! molecular entity - -[Term] -id: MS:1003034 -name: atom -def: "Smallest constituent unit of ordinary matter that constitutes a chemical element." [https://en.wikipedia.org/wiki/Atom] -is_a: MS:1000881 ! molecular entity - -[Term] -id: MS:1003035 -name: small molecule -def: "Low molecular weight (< 900 daltons) organic compound that may regulate a biological process." [https://en.wikipedia.org/wiki/Small_molecule] -is_a: MS:1000859 ! molecule - -[Term] -id: MS:1003036 -name: metabolite -def: "Small molecule that is the intermediate end product of metabolism." [https://en.wikipedia.org/wiki/Metabolite] -is_a: MS:1003035 ! small molecule - -[Term] -id: MS:1003037 -name: ribonucleotide -def: "Nucleotide containing ribose as its pentose component." [https://en.wikipedia.org/wiki/Ribonucleotide] -is_a: MS:1003035 ! small molecule - -[Term] -id: MS:1003038 -name: deoxyribonucleotide -def: "Monomer, or single unit, of DNA, or deoxyribonucleic acid." [https://en.wikipedia.org/wiki/Deoxyribonucleotide] -is_a: MS:1003035 ! small molecule - -[Term] -id: MS:1003039 -name: amino acid -def: "Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid." [https://en.wikipedia.org/wiki/Amino_acid] -is_a: MS:1003035 ! small molecule - -[Term] -id: MS:1003040 -name: monosaccharide -def: "Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule." [https://en.wikipedia.org/wiki/Monosaccharide] -is_a: MS:1003035 ! small molecule - -[Term] -id: MS:1003041 -name: nucleic acid -def: "Molecule composed of a chain of nucleotides." [https://en.wikipedia.org/wiki/Nucleic_acid] -is_a: MS:1000859 ! molecule - -[Term] -id: MS:1003042 -name: polysaccharide -def: "Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages." [https://en.wikipedia.org/wiki/Polysaccharide] -is_a: MS:1000859 ! molecule - -[Term] -id: MS:1003043 -name: number of residues -def: "Number of amino acid residues in a peptide, commonly referred to as the peptide length." [PSI:PI] -is_a: MS:1000887 ! peptide attribute - -[Term] -id: MS:1003044 -name: number of missed cleavages -def: "Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not." [PSI:PI] -is_a: MS:1000887 ! peptide attribute - -[Term] -id: MS:1003045 -name: peptide-to-protein mapping -def: "Process of mapping a peptide sequence to a protein sequence." [PSI:PI] -is_a: MS:1000887 ! peptide attribute - -[Term] -id: MS:1003046 -name: peptide-to-protein mapping attribute -def: "Nonphysical characteristic attributed to the result of peptide-to-protein mapping." [PSI:PI] -is_a: MS:1003045 ! peptide-to-protein mapping - -[Term] -id: MS:1003047 -name: protein sequence offset -def: "Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence." [PSI:PI] -is_a: MS:1003046 ! peptide-to-protein mapping attribute - -[Term] -id: MS:1003048 -name: number of enzymatic termini -def: "Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules." [PSI:PI] -is_a: MS:1003046 ! peptide-to-protein mapping attribute - -[Term] -id: MS:1003049 -name: peptidoform -def: "Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations." [PSI:PI] -is_a: MS:1000860 ! peptide - -[Term] -id: MS:1003050 -name: peptidoform attribute -def: "Non-inherent characteristic attributed to a peptidoform." [PSI:PI] -relationship: part_of MS:1003049 ! peptidoform - -[Term] -id: MS:1003051 -name: peptidoform ion -def: "Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'." [PSI:PI] -is_a: MS:1003049 ! peptidoform -synonym: "precursor" RELATED [] -synonym: "precursor ion" RELATED [] -synonym: "parent ion" RELATED [] - -[Term] -id: MS:1003052 -name: peptidoform ion property -def: "Inherent or measurable characteristic of a peptidoform ion." [PSI:PI] -relationship: part_of MS:1003051 ! peptidoform ion - -[Term] -id: MS:1003053 -name: theoretical monoisotopic m/z -def: "Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents." [PSI:PI] -is_a: MS:1003052 ! peptidoform ion property - -[Term] -id: MS:1003054 -name: theoretical average m/z -def: "Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes." [PSI:PI] -is_a: MS:1003052 ! peptidoform ion property - -[Term] -id: MS:1003055 -name: adduct -def: "Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species." [https://en.wikipedia.org/wiki/Adduct] -is_a: MS:1000859 ! molecule - -[Term] -id: MS:1003056 -name: adduct ion property -def: "Physical measurable characteristic of an adduct ion." [PSI:PI] -relationship: part_of MS:1000353 ! adduct ion - -[Term] -id: MS:1003057 -name: scan number -def: "Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run." [PSI:PI] -is_a: MS:1000503 ! scan attribute - -[Term] -id: MS:1003058 -name: spectrum property -def: "Inherent or measurable characteristic of a spectrum." [PSI:PI] -relationship: part_of MS:1000442 ! spectrum - -[Term] -id: MS:1003059 -name: number of peaks -def: "Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points." [PSI:PI] -is_a: MS:1003058 ! spectrum property - -[Term] -id: MS:1003060 -name: number of data points -def: "Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks." [PSI:PI] -is_a: MS:1003058 ! spectrum property - -[Term] -id: MS:1003061 -name: spectrum name -def: "Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection." [PSI:PI] -is_a: MS:1000499 ! spectrum attribute - -[Term] -id: MS:1003062 -name: spectrum index -def: "Integer index value associated with a spectrum within a collection of spectra, often in a spectral library. By custom, index counters should begin with 0." [PSI:PI] -is_a: MS:1000499 ! spectrum attribute - -[Term] -id: MS:1003063 -name: universal spectrum identifier -def: "PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library." [PSI:PI] -is_a: MS:1000499 ! spectrum attribute - -[Term] -id: MS:1003064 -name: spectrum aggregation attribute -def: "Non-inherent characteristic attributed to spectrum aggregation." [PSI:PI] -is_a: MS:1000499 ! spectrum attribute - -[Term] -id: MS:1003065 -name: spectrum aggregation type -def: "Categorization of a spectrum based on its type of aggregation (e.g., individual spectrum, consensus spectrum, best replicate spectrum, etc.)." [PSI:PI] -is_a: MS:1003064 ! spectrum aggregation attribute - -[Term] -id: MS:1003066 -name: singleton spectrum -def: "Spectrum that is not the result of some aggregation process." [PSI:PI] -is_a: MS:1003065 ! spectrum aggregation type - -[Term] -id: MS:1003067 -name: consensus spectrum -def: "Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates." [PSI:PI] -is_a: MS:1003065 ! spectrum aggregation type - -[Term] -id: MS:1003068 -name: best replicate spectrum -def: "Spectrum that is considered the most representative from a pool of replicate spectra." [PSI:PI] -is_a: MS:1003065 ! spectrum aggregation type - -[Term] -id: MS:1003069 -name: number of replicate spectra available -def: "Number of replicate spectra available for use during the aggregation process." [PSI:PI] -is_a: MS:1003064 ! spectrum aggregation attribute - -[Term] -id: MS:1003070 -name: number of replicate spectra used -def: "Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm." [PSI:PI] -is_a: MS:1003064 ! spectrum aggregation attribute - -[Term] -id: MS:1003071 -name: spectrum origin attribute -def: "Non-inherent characteristic attributed to spectrum aggregation." [PSI:PI] -is_a: MS:1000499 ! spectrum attribute - -[Term] -id: MS:1003072 -name: spectrum origin type -def: "Categorization of a spectrum based on its origin (e.g., observed spectrum, predicted spectrum, demultiplexed spectrum, etc.)." [PSI:PI] -is_a: MS:1003071 ! spectrum origin attribute - -[Term] -id: MS:1003073 -name: observed spectrum -def: "Spectrum that originates from an analysis attempt of a single analyte species on an instrument." [PSI:PI] -is_a: MS:1003072 ! spectrum origin type - -[Term] -id: MS:1003074 -name: predicted spectrum -def: "Spectrum that originates from a compututational algorithm that attempts to predict spectra." [PSI:PI] -is_a: MS:1003072 ! spectrum origin type - -[Term] -id: MS:1003075 -name: demultiplexed spectrum -def: "Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species." [PSI:PI] -is_a: MS:1003072 ! spectrum origin type - -[Term] -id: MS:1003076 -name: uninterpreted spectrum -def: "Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features." [PSI:PI] -is_a: MS:1000442 ! spectrum - -[Term] -id: MS:1003077 -name: interpreted spectrum -def: "Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature." [PSI:PI] -is_a: MS:1000442 ! spectrum - -[Term] -id: MS:1003078 -name: interpreted spectrum attribute -def: "Non-inherent characteristic attributed to an interpreted spectrum." [PSI:PI] -relationship: part_of MS:1003077 ! interpreted spectrum - -[Term] -id: MS:1003079 -name: total unassigned intensity fraction -def: "Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum." [PSI:PI] -is_a: MS:1003078 ! interpreted spectrum attribute - -[Term] -id: MS:1003080 -name: top 20 peak unassigned intensity fraction -def: "Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum." [PSI:PI] -is_a: MS:1003078 ! interpreted spectrum attribute - -[Term] -id: MS:1003081 -name: unidentified modification monoisotopic mass delta -def: "Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the element in mzIdentML." [PSI:PI] -is_a: MS:1001471 ! peptide modification details -xref: value-type:xsd\:double "The allowed value-type for this CV term." -relationship: has_units UO:0000221 ! dalton -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003082 -name: MS-DIAL -def: "Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors." [PMID:25938372] -is_a: MS:1002878 ! small molecule analysis software -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1003083 -name: raw data file -def: "Data file that contains original data as generated by an instrument, although not necessarily in the original data format (i.e. an original raw file converted to a different format is still a raw data file)." [PSI:MS] -is_a: MS:1000577 ! source data file - -[Term] -id: MS:1003084 -name: processed data file -def: "File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000577 ! source data file -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1003085 -name: previous MSn-1 scan precursor intensity -def: "Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001141 ! intensity of precursor ion -is_a: MS:1000499 ! spectrum attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1003086 -name: precursor apex intensity -def: "Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1001141 ! intensity of precursor ion -is_a: MS:1000499 ! spectrum attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1003087 -name: supported by repository but incomplete data and/or metadata -def: "Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. However, some metadata is not properly described due to lack of CV terms or some auxiliary data, such as data used to create a spectral library or a sequence search database crucial to the analysis, is not available." [PSI:PI] -is_a: MS:1002844 ! Experiment additional parameter - -[Term] -id: MS:1003088 -name: truncation and zlib compression -def: "Data array compression using mantissa bit truncation followed by zlib compression." [https://github.com/biospi/pwiz] -is_a: MS:1000572 ! binary data compression type - -[Term] -id: MS:1003089 -name: truncation, delta prediction and zlib compression -def: "Data array compression using mantissa bit truncation, delta prediction and zlib compression." [https://github.com/biospi/pwiz] -is_a: MS:1000572 ! binary data compression type - -[Term] -id: MS:1003090 -name: truncation, linear prediction and zlib compression -def: "Data array compression using mantissa bit truncation, linear prediction and zlib compression." [https://github.com/biospi/pwiz] -is_a: MS:1000572 ! binary data compression type - -[Term] -id: MS:1003091 -name: binary data compression parameter -def: "Settable parameter for a binary data compression event." [PSI:MS] -relationship: part_of MS:1000442 ! spectrum -relationship: part_of MS:1000625 ! chromatogram - -[Term] -id: MS:1003092 -name: number of mantissa bits truncated -def: "Number of extraneous mantissa bits truncated to improve subsequent compression." [PSI:MS] -xref: value-type:xsd\:positiveInteger "Number of mantissa bits truncated." -is_a: MS:1003091 ! binary data compression parameter -relationship: has_value_type xsd\:positiveInteger ! The allowed value-type for this CV term - -[Term] -id: MS:1003093 -name: Lys-N -def: "Metalloendopeptidase found in the mushroom Grifola frondosa that cleaves proteins on the amino side of lysine residues." [https://en.wikipedia.org/wiki/Lys-N] -is_a: MS:1001045 ! cleavage agent name -relationship: has_regexp MS:1001335 ! (?=K) - -[Term] -id: MS:1003094 -name: Orbitrap Exploris 240 -def: "Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1003095 -name: Orbitrap Exploris 120 -def: "Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS." [PSI:PI] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1003096 -name: LTQ Orbitrap Velos Pro -def: "Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1003097 -name: MaxQuant protein group-level score -def: "The probability based MaxQuant protein group score." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002368 ! search engine specific score for protein groups -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003098 -name: Andromeda peptide PEP -def: "Peptide probability from Andromeda." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003099 -name: MaxQuant-DIA peptide PEP -def: "Peptide probability from MaxQuant-DIA algorithm." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003100 -name: MaxQuant-DIA score -def: "PSM evidence score from MaxQuant-DIA algorithm." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003101 -name: MaxQuant-DIA PEP -def: "PSM evidence PEP probability from MaxQuant-DIA algorithm." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003102 -name: NIST msp comment -def: "Term for a comment field withing the NIST msp file format" [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000499 ! spectrum attribute -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1003103 -name: ion interpretation format -def: "Interpretation format used for annotating individual spectrum ion peaks." [PSI:MS] -is_a: MS:1003078 ! interpreted spectrum attribute - -[Term] -id: MS:1003104 -name: peptide ion interpretation format -def: "Interpretation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions." [PSI:MS] -is_a: MS:1003103 ! ion interpretation format - -[Term] -id: MS:1003105 -name: cross-linked peptide ion interpretation format -def: "Interpretation format designed specifically for cross-linked peptide ion peaks." [PSI:MS] -is_a: MS:1003103 ! ion interpretation format - -[Term] -id: MS:1003106 -name: glycan ion interpretation format -def: "Interpretation format designed specifically for glycan ion peaks." [PSI:MS] -is_a: MS:1003103 ! ion interpretation format - -[Term] -id: MS:1003107 -name: lipid ion interpretation format -def: "Interpretation format designed specifically for lipid ion peaks." [PSI:MS] -is_a: MS:1003103 ! ion interpretation format - -[Term] -id: MS:1003108 -name: PatternLab -def: "PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data." [PSI:MS] -is_a: MS:1001139 ! quantitation software name -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1003109 -name: SIM-XL -def: "Identifying cross-linked peptides in complex protein mixtures" [PSI:MS] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1003110 -name: SIM-XL score -def: "SIM-XL identification search engine score" [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003111 -name: QUIN-XL -def: "Quantification of cross-linked peptides in complex protein mixtures" [PSI:MS] -is_a: MS:1001139 ! quantitation software name - -[Term] -id: MS:1003112 -name: Orbitrap ID-X -def: "Thermo Scientific Orbitrap ID-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:MS] -is_a: MS:1000494 ! Thermo Scientific instrument model - -[Term] -id: MS:1003113 -name: OpenMS:ConsensusID PEP -def: "The OpenMS ConsesusID tool posterior error probability" [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003114 -name: OpenMS:Best PSM Score -def: "The score of the best PSM selected by the underlying identification tool" [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003115 -name: OpenMS:Target-decoy PSM q-value -def: "The OpenMS Target-decoy q-values at PSM level" [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003116 -name: OpenMS:Target-decoy peptide q-value -def: "The OpenMS Target-decoy q-values at peptide sequence level" [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003117 -name: OpenMS:Target-decoy protein q-value -def: "The OpenMS Target-decoy q-values at protein level" [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003118 -name: EPIFANY -def: "A Method for Efficient High-Confidence Protein Inference. The tool is part of the OpenMS framework" [PSI:MS] -is_a: MS:1001456 ! analysis software -is_a: MS:1000752 ! TOPP software - -[Term] -id: MS:1003119 -name: EPIFANY:Protein posterior probability -def: "Protein Posterior probability calculated by EPIFANY protein inference algorithm" [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002363 ! search engine specific score for proteins -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003120 -name: OpenMS:LFQ intensity -def: "The data type LFQ intensity produced by OpenMS." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003121 -name: OpenMS:LFQ spectral count -def: "The data type LFQ spectral count produced by OpenMS." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001805 ! quantification datatype -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003122 -name: rapifleX -def: "Bruker Daltonics' rapiflex: MALDI TOF/TOF." [PSI:MS] -is_a: MS:1001534 ! Bruker Daltonics flex series - -[Term] -id: MS:1003123 -name: Bruker Daltonics timsTOF series -def: "Bruker Daltonics timsTOF series" [PSI:MS] -is_a: MS:1000122 ! Bruker Daltonics instrument model - -[Term] -id: MS:1003124 -name: timsTOF fleX -def: "Bruker Daltonics' timsTOF fleX" [PSI:MS] -is_a: MS:1003123 ! Bruker Daltonics timsTOF series - -[Term] -id: MS:1003125 -name: ProSight:spectral Q-value -def: "ProSight spectrum-level Q-value." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002354 ! PSM-level q-value -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003126 -name: ProSight:spectral P-score -def: "ProSight spectrum-level P-score." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003127 -name: ProSight:spectral E-value -def: "ProSight spectrum-level E-value." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002353 ! PSM-level e-value -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003128 -name: ProSight:spectral C-score -def: "ProSight spectrum-level C-score." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001143 ! PSM-level search engine specific statistic -relationship: has_order MS:1002108 ! higher score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003129 -name: proteoform-level Q-value -def: "Estimation of the Q-value for proteoforms." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002905 ! proteoform-level identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003130 -name: ProSight:proteoform Q-value -def: "ProSight proteoform-level Q-value." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1003129 ! proteoform-level Q-value -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003131 -name: isoform-level identification attribute -def: "Isoform level information." [PSI:MS] -is_a: MS:1002694 ! single identification result attribute - -[Term] -id: MS:1003132 -name: isoform-level identification statistic -def: "Identification confidence metric for a isoform." [PSI:MS] -is_a: MS:1003131 ! isoform-level identification attribute - -[Term] -id: MS:1003133 -name: isoform-level Q-value -def: "Estimation of the Q-value for isoforms." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1003132 ! isoform-level identification statistic -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003134 -name: ProSight:isoform Q-value -def: "ProSight isoform-level Q-value." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1003133 ! isoform-level Q-value -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003135 -name: ProSight:protein Q-value -def: "ProSight protein-level Q-value." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1001869 ! protein-level q-value -relationship: has_order MS:1002109 ! lower score better -relationship: has_value_type xsd\:double ! The allowed value-type for this CV term - -[Term] -id: MS:1003136 -name: ProSight input parameter -def: "Search engine input parameters specific to ProSight." [PSI:MS] -is_a: MS:1001302 ! search engine specific input parameter - -[Term] -id: MS:1003137 -name: TDPortal input parameter -def: "Search engine input parameters specific to TDPortal." [PSI:MS] -is_a: MS:1001302 ! search engine specific input parameter - -[Term] -id: MS:1003138 -name: ProSight:Run delta m mode -def: "If true, runs delta m mode in ProSight." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1003136 ! ProSight input parameter -is_a: MS:1003137 ! TDPortal input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1003139 -name: ProSight:Run Subsequence Search mode -def: "If true, runs Subsequence Search mode in ProSight." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1003136 ! ProSight input parameter -is_a: MS:1003137 ! TDPortal input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1003140 -name: ProSight:Run Annotated Proteoform Search mode -def: "If true, runs Annotated Proteoform Search mode in ProSight." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -is_a: MS:1003136 ! ProSight input parameter -is_a: MS:1003137 ! TDPortal input parameter -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: MS:1003141 -name: ProSight -def: "ProSight: Database search engine for top-down proteomics." [PSI:MS] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1003142 -name: TDPortal -def: "TDPortal: Database search engine for top-down proteomics." [PSI:MS] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1003143 -name: mass array -def: "A data array of mass values." [PSI:MS] -xref: binary-data-type:MS\:1000521 "32-bit float" -xref: binary-data-type:MS\:1000523 "64-bit float" -is_a: MS:1000513 ! binary data array -relationship: has_units UO:0000221 ! dalton - -[Term] -id: MS:1003144 -name: Triple Quad 7500 -def: "SCIEX Triple Quad 7500." [PSI:MS] -is_a: MS:1000121 ! SCIEX instrument model - -[Term] -id: MS:1003145 -name: ThermoRawFileParser -def: "Cross-platform software to convert Thermo RAW files to a number of open formats." [DOI:10.1021/acs.jproteome.9b00328, PMID:31755270] -is_a: MS:1001457 ! data processing software - -[Term] -id: MS:1003146 -name: pyteomics -def: "Python module that helps handling various proteomics data analysis tasks." [DOI:10.1021/acs.jproteome.8b00717, PMID:30576148] -is_a: MS:1001456 ! analysis software - -[Term] -id: MS:1003147 -name: PTMProphet probability -def: "Probability that one mass modification has been correctly localized to a specific residue as computed by PTMProphet." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring - -[Term] -id: MS:1003148 -name: PTMProphet mean best probability -def: "PSM-specific average of the m best site probabilities over all potential sites where m is the number of modifications of a specific type, as computed by PTMProphet." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring - -[Term] -id: MS:1003149 -name: PTMProphet normalized information content -def: " PTMProphet-computed PSM-specific normalized (0.0 – 1.0) measure of information content across all modifications of a specific type." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring - -[Term] -id: MS:1003150 -name: PTMProphet information content -def: " PTMProphet-computed PSM-specific measure of information content per modification type ranging from 0 to m, where m is the number of modifications of a specific type." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] -is_a: MS:1001968 ! PTM localization PSM-level statistic -relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring - -[Term] -id: MS:1003151 -name: SHA-256 -def: "SHA-256 (member of Secure Hash Algorithm-2 family) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000561 ! data file checksum type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: MS:1003152 -name: GCMS-QP2010SE -def: "Shimadzu Scientific Instruments GCMS-QP2010SE." [PSI:MS] -is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model - -[Term] -id: MS:1003153 -name: raw ion mobility drift time array -def: "Array of raw ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002893 ! ion mobility array -relationship: has_units UO:0000028 ! millisecond -relationship: has_units UO:0000010 ! second -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1003154 -name: deconvoluted ion mobility array -def: "Array of ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002893 ! ion mobility array -relationship: has_units UO:0000028 ! millisecond -relationship: has_units UO:0000010 ! second -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1003155 -name: deconvoluted inverse reduced ion mobility array -def: "Array of ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002893 ! ion mobility array -relationship: has_units MS:1002814 ! volt-second per square centimeter -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1003156 -name: deconvoluted ion mobility drift time array -def: "Array of mean ion mobility values from a drift time device, reported in seconds (or milliseconds), as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1002893 ! ion mobility array -relationship: has_units UO:0000028 ! millisecond -relationship: has_units UO:0000010 ! second -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1003157 -name: scanning quadrupole position lower bound m/z array -def: "Array of m/z values representing the lower bound m/z of the quadrupole position at each point in the spectrum." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000513 ! binary data array -relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1003158 -name: scanning quadrupole position upper bound m/z array -def: "Array of m/z values representing the upper bound m/z of the quadrupole position at each point in the spectrum." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000513 ! binary data array -relationship: has_units MS:1000040 ! m/z -relationship: has_value_type xsd\:float ! The allowed value-type for this CV term - -[Term] -id: MS:1003159 -name: isolation window full range -def: "Indicates an acquisition mode in which the isolation window is a full range, rather than a subset of the full range." [PSI:MS] -is_a: MS:1000792 ! isolation window attribute - -[Term] -id: MS:1003160 -name: mzQC format -def: "Proteomics Standards Initiative mzQC format for quality control data." [PSI:MS] -is_a: MS:1003161 ! quality control data format - -[Term] -id: MS:1003161 -name: quality control data format -def: "Grouping term for quality control data formats." [PSI:MS] -is_a: MS:1001459 ! file format - -[Term] -id: MS:1003162 -name: PTX-QC -def: "Proteomics (PTX) - QualityControl (QC) software for QC report generation and visualization." [DOI:10.1021/acs.jproteome.5b00780, PMID:26653327, https://github.com/cbielow/PTXQC/] -is_a: MS:1001456 ! analysis software -synonym: "PTXQC" EXACT [] - -[Term] -id: MS:1003163 -name: analyte mixture members -def: "The set of analyte identifiers that compose an interpretation of a spectrum." [PSI:PI] -is_a: MS:1003078 ! interpreted spectrum attribute -relationship: has_value_type MS:1002712 ! list of integers - -[Term] -id: PEFF:0000001 -name: PEFF CV term -def: "PSI Extended FASTA Format controlled vocabulary term." [PSI:PEFF] -relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies - -[Term] -id: PEFF:0000002 -name: PEFF file header section term -def: "CV term that may appear in a PEFF file header section." [PSI:PEFF] -is_a: PEFF:0000001 ! PEFF CV term - -[Term] -id: PEFF:0000003 -name: PEFF file sequence entry term -def: "CV term that may appear in a description line of a PEFF file individual sequence entry." [PSI:PEFF] -is_a: PEFF:0000001 ! PEFF CV term - -[Term] -id: PEFF:0000008 -name: DbName -def: "PEFF keyword for the sequence database name." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0000009 -name: Prefix -def: "PEFF keyword for the sequence database prefix." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0000010 -name: DbDescription -def: "PEFF keyword for the sequence database short description." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0000011 -name: Decoy -def: "PEFF keyword for the specifying whether the sequence database is a decoy database." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." -relationship: has_value_type xsd\:boolean ! The allowed value-type for this CV term - -[Term] -id: PEFF:0000012 -name: DbSource -def: "PEFF keyword for the source of the database file." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0000013 -name: DbVersion -def: "PEFF keyword for the database version (release date) according to database provider." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0000014 -name: DbDate -def: "OBSOLETE PEFF keyword for the database date (release or file date of the source) according to database provider." [PSI:PEFF] -comment: This term was obsoleted. -is_a: PEFF:0000002 ! PEFF file header section term -is_obsolete: true - -[Term] -id: PEFF:0000015 -name: NumberOfEntries -def: "PEFF keyword for the sumber of sequence entries in the database." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:integer "The allowed value-type for this CV term." -relationship: has_value_type xsd\:integer ! The allowed value-type for this CV term - -[Term] -id: PEFF:0000016 -name: Conversion -def: "PEFF keyword for the description of the conversion from original format to this current one." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0000017 -name: SequenceType -def: "PEFF keyword for the molecular type of the sequences." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_regexp PEFF:1002002 ! regular expression for PEFF molecular sequence type -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0000018 -name: SpecificKey -def: "PEFF keyword for database specific keywords not included in the current controlled vocabulary." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0000019 -name: SpecificValue -def: "PEFF keyword for the specific values for a custom key." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0000020 -name: DatabaseDescription -def: "PEFF keyword for the short description of the PEFF file." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0000021 -name: GeneralComment -def: "PEFF keyword for a general comment." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0000022 -name: ProteoformDb -def: "PEFF keyword that when set to 'true' indicates that the database contains complete proteoforms." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0000023 -name: OptionalTagDef -def: "PEFF keyword for the short tag (abbreviation) and longer definition used to annotate a sequence annotation (such as variant or modification) in the OptionalTag location." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0000024 -name: HasAnnotationIdentifiers -def: "PEFF keyword that when set to 'true' indicates that entries in the database have identifiers for each annotation." [PSI:PEFF] -is_a: PEFF:0000002 ! PEFF file header section term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001001 -name: DbUniqueId -def: "OBSOLETE Sequence database unique identifier." [PSI:PEFF] -comment: This term was made obsolete because decided in Heidelberg 2018-04 that this is redundant. -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001002 -name: PName -def: "PEFF keyword for the protein full name." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001003 -name: NcbiTaxId -def: "PEFF keyword for the NCBI taxonomy identifier." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:int "The allowed value-type for this CV term." -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001004 -name: TaxName -def: "PEFF keyword for the taxonomy name (latin or common name)." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001005 -name: GName -def: "PEFF keyword for the gene name." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001006 -name: Length -def: "PEFF keyword for the sequence length." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:int "The allowed value-type for this CV term." -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001007 -name: SV -def: "PEFF keyword for the sequence version." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001008 -name: EV -def: "PEFF keyword for the entry version." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001009 -name: PE -def: "PEFF keyword for the Protein Evidence; A UniProtKB code 1-5." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:int "The allowed value-type for this CV term." -relationship: has_value_type xsd\:int ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001010 -name: Processed -def: "PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001011 -name: Variant -def: "OBSOLETE Sequence variation (substitution, insertion, deletion)." [PSI:PEFF] -comment: This term was made obsolete in favor of VariantSimple and VariantComplex. -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -is_obsolete: true -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001012 -name: ModResPsi -def: "PEFF keyword for the modified residue with PSI-MOD identifier." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001013 -name: ModRes -def: "PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001014 -name: AltAC -def: "PEFF keyword for the Alternative Accession Code." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001015 -name: SeqStatus -def: "PEFF keyword for the sequence status. Complete or Fragment." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_regexp PEFF:1002003 ! regular expression for PEFF sequence status -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001016 -name: CC -def: "PEFF keyword for the entry associated comment." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001017 -name: KW -def: "PEFF keyword for the entry associated keyword(s)." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001018 -name: GO -def: "PEFF keyword for the Gene Ontology code." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001019 -name: XRef -def: "PEFF keyword for the cross-reference to an external resource." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001020 -name: mature protein -def: "Portion of a newly synthesized protein that contributes to a final structure after other components such as signal peptides are removed." [PSI:PEFF] -is_a: PEFF:0001032 ! PEFF molecule processing keyword -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001021 -name: signal peptide -def: "Short peptide present at the N-terminus of a newly synthesized protein that is cleaved off and is not part of the final mature protein." [PSI:PEFF] -is_a: PEFF:0001032 ! PEFF molecule processing keyword -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001022 -name: transit peptide -def: "Short peptide present at the N-terminus of a newly synthesized protein that helps the protein through the membrane of its destination organelle." [PSI:PEFF] -is_a: PEFF:0001032 ! PEFF molecule processing keyword -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001023 -name: Conflict -def: "PEFF keyword for the sequence conflict; a UniProtKB term." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001024 -name: Crc64 -def: "PEFF keyword for the Sequence checksum in crc64." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001025 -name: Domain -def: "PEFF keyword for the sequence range of a domain." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001026 -name: ID -def: "PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001027 -name: ModResUnimod -def: "PEFF keyword for the modified residue with UniMod identifier." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001028 -name: VariantSimple -def: "PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001029 -name: VariantComplex -def: "PEFF keyword for a sequence variation that is more complex than a single amino acid change or change to a stop codon." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001030 -name: Proteoform -def: "PEFF keyword for the proteoforms of this protein, constructed as a set of annotation identifiers." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001031 -name: DisulfideBond -def: "PEFF keyword for the disulfide bonds in this protein, constructed as a sets of annotation identifiers of two half-cystine modifications." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001032 -name: PEFF molecule processing keyword -def: "PEFF keyword describing the type of processing event being described." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term - -[Term] -id: PEFF:0001033 -name: Comment -def: "PEFF keyword for the individual protein entry comment. It is discouraged to put parsable information here. This is only for free-text commentary." [PSI:PEFF] -is_a: PEFF:0000003 ! PEFF file sequence entry term -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001034 -name: propeptide -def: "Short peptide that is cleaved off a newly synthesized protein and generally immediately degraded in the process of protein maturation, and is not a signal peptide or transit peptide." [PSI:PEFF] -is_a: PEFF:0001032 ! PEFF molecule processing keyword -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:0001035 -name: initiator methionine -def: "N-terminal methionine residue of a protein that can be co-translationally cleaved." [PSI:PEFF] -is_a: PEFF:0001032 ! PEFF molecule processing keyword -xref: value-type:xsd\:string "The allowed value-type for this CV term." -relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -relationship: has_value_type xsd\:string ! The allowed value-type for this CV term - -[Term] -id: PEFF:1002001 -name: regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment -def: "([0-9]+|[A-Z*](|.+)?)." [PSI:PEFF] -is_a: MS:1002479 ! regular expression - -[Term] -id: PEFF:1002002 -name: regular expression for PEFF molecular sequence type -def: "(AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+)." [PSI:PEFF] -is_a: MS:1002479 ! regular expression - -[Term] -id: PEFF:1002003 -name: regular expression for PEFF sequence status -def: "(Complete|Fragment|[a-z0-9A-Z]+)." [PSI:PEFF] -is_a: MS:1002479 ! regular expression diff --git a/implementations/python/mzlib/ontology.py b/implementations/python/mzlib/ontology.py deleted file mode 100644 index 8213831..0000000 --- a/implementations/python/mzlib/ontology.py +++ /dev/null @@ -1,69 +0,0 @@ -import logging - -from psims.controlled_vocabulary import Entity -from psims.controlled_vocabulary.controlled_vocabulary import load_uo, load_unimod, load_psims - -logger = logging.getLogger(__name__) -logger.addHandler(logging.NullHandler()) - - -class _VocabularyResolverMixin(object): - default_cv_loader_map = { - "MS": load_psims, - "UO": load_uo, - "UNIMOD": load_unimod, - } - - def __init__(self, *args, **kwargs): - self.controlled_vocabularies = dict() - super().__init__(*args, **kwargs) - - def load_cv(self, name): - if name in self.controlled_vocabularies: - return self.controlled_vocabularies[name] - self.controlled_vocabularies[name] = self.default_cv_loader_map[name]() - return self.controlled_vocabularies[name] - - def find_term_for(self, curie: str) -> Entity: - try: - name, _id = curie.split(":") - except ValueError as err: - raise KeyError(curie) from err - cv = self.load_cv(name) - term = cv[curie] - return term - - def find_term_by_name(self, name: str) -> Entity: - cv_keys = ['MS', 'UNIMOD'] - for cv_key in cv_keys: - cv = self.load_cv(cv_key) - try: - term = cv[name] - return term - except KeyError: - continue - raise KeyError(name) - - -class ControlledVocabularyResolver(_VocabularyResolverMixin): - - def name_to_curie(self, name: str) -> str: - term = self.find_term_by_name(name) - return term.id - - def attribute_syntax(self, name: str) -> str: - if self.is_curie(name): - if "|" in name: - return name - term = self.find_term_for(name) - else: - term = self.find_term_by_name(name) - return f"{term.id}|{term.name}" - - def is_curie(self, name: str) -> bool: - if ':' not in name: - return False - prefix, _rest = name.split(":") - if prefix in self.default_cv_loader_map: - return True - return False diff --git a/implementations/python/mzlib/ontology_term.py b/implementations/python/mzlib/ontology_term.py deleted file mode 100644 index 5a96750..0000000 --- a/implementations/python/mzlib/ontology_term.py +++ /dev/null @@ -1,465 +0,0 @@ -#!/usr/bin/env python3 -# pragma: no cover -#from __future__ import print_function -#import sys -#def eprint(*args, **kwargs): -# print(*args, file=sys.stderr, **kwargs) - -import logging -import re -import sys - -############################################################################# -#### Ontology Term class -class OntologyTerm(object): - - - ######################################################################### - #### Constructor - def __init__(self, line_list=None, verbose=0): - - self.line_list = [] - self.verbose = verbose - - self.is_valid = False - self.prefix = None - self.identifier = None - self.curie = None - self.name = None - self.value_type = None - self.definition = None - self.origin = None - self.unparsable_line_list = [] - self.origin = None - self.xref_list = [] - self.relationship_list = [] - self.parents = [] - self.children = [] - self.synonyms = [] - self.xrefs = [] - self.has_units = [] - self.has_order = None - self.has_domain = None - self.has_regexp = None - self.is_obsolete = False - self.namespaces = [] - self.subsets = [] - - #### Mass modification-related properties - self.monoisotopic_mass = None - self.average_mass = None - self.sites = {} - self.extended_name = None - - self.n_errors = 0 - self.error_code = None - self.error_message = None - - #### If we have been given an input line_list on construction, parse it right away - if line_list is not None: - self.parse(line_list=line_list) - - - ######################################################################### - #### parse the line_list - def parse(self, line_list=None, verbose=0): - verboseprint = print if verbose>1 else lambda *a, **k: None - if verbose > 1: - logger = logging.getLogger() - logger.setLevel(logging.DEBUG) - - #### Make sure there is a line_list to parse - if line_list is not None: - self.line_list = line_list - - #### Loop over the lines, processing each one - for line in self.line_list: - - #### Just skip the [Term] line - match = re.search("^\s*\[Term\]\s*$",line) - if match: continue - - has_match = False - - ############################# - #### Process the id line - match = re.search("^\s*id:",line) - if match: - match = re.search("^\s*id:\s*(\S+)\s*$",line) - if match: - self.curie = match.groups()[0] - if ":" in self.curie: - self.prefix,self.identifier = self.curie.split(":",1) - has_match = True - else: - #logging.error("Unable to parse '%s'", line) - self.prefix = '' - self.identifier = self.curie - has_match = True - else: - self.set_error("TermIdError",f"Unable to parse id line '{line}'") - - ############################# - #### Process the name line - match = re.search("^\s*name:",line) - if match: - match = re.search("^\s*name:\s*(.+)\s*$",line) - if match: - self.name = match.groups()[0] - has_match = True - else: - self.set_error("TermNameError",f"Unable to parse id line '{line}'") - - ############################# - #### Process the def line - match = re.search("^\s*def:",line) - if match: - match = re.search("^\s*def:\s*(.+)\s*$",line) - if match: - self.definition = match.groups()[0] - has_match = True - match = re.search('^"(.+)"\s*\[(.*)\].*$',self.definition) - if match: - self.definition = match.groups()[0] - self.origin = match.groups()[1] - else: - logging.error("Unable to parse definition string '%s'", self.definition) - has_match = True - else: - self.set_error("TermDefinitionError",f"Unable to parse def line '{line}'") - - ############################# - #### Process the value-type line - match = re.search("^\s*xref: value-type",line) - if match: - if self.value_type is not None: - logging.error("This term already has a type at line '%s'", line) - match = re.search("^\s*xref: value-type:(\S+)",line) - if match: - self.value_type = match.groups()[0] - has_match = True - else: - self.set_error("TermValueTypeError",f"Unable to parse value-type line '{line}'") - - ############################# - #### Process the binary-data-type line - match = re.search("^\s*xref: binary-data-type",line) - if match: - match = re.search("^\s*xref: binary-data-type:(\S+)",line) - if match: - pass - has_match = True - else: - self.set_error("TermBinaryDataTypeError",f"Unable to parse binary-data-type line '{line}'") - - ############################# - #### Process the is_a line - match = re.search("^\s*is_a",line) - if match: - match = re.search("^\s*is_a:\s*(\S+)",line) - if match: - self.parents.append( { "type": "is_a", "curie": match.groups()[0] } ) - has_match = True - else: - self.set_error("TermIsAError",f"Unable to parse is_a line '{line}'") - - ############################# - #### Process the part_of line - match = re.search("^relationship: part_of",line) - if match: - match = re.search("^\s*relationship:\s*part_of\s*(\S+)",line) - if match: - self.parents.append( { "type": "part_of", "curie": match.groups()[0] } ) - has_match = True - else: - self.set_error("TermPartOfError",f"Unable to parse part_of line '{line}'") - - ############################# - #### Process the has_units line - match = re.search("has_units",line) - if match: - match = re.search("^\s*relationship: has_units\s+(\S+)",line) - if match: - self.has_units.append(match.groups()[0]) - has_match = True - else: - self.set_error("TermHasUnitsError",f"Unable to parse has_units line '{line}'") - - ############################# - #### Process the has_order line - match = re.search("has_order",line) - if match: - match = re.search("^\s*relationship: has_order\s+(\S+)",line) - if match: - self.has_order = match.groups()[0] - has_match = True - else: - self.set_error("TermHasOrderError",f"Unable to parse has_order line '{line}'") - - ############################# - #### Process the has_domain line - match = re.search("has_domain",line) - if match: - match = re.search("^\s*relationship: has_domain\s+(\S+)",line) - if match: - self.has_domain = match.groups()[0] - has_match = True - else: - self.set_error("TermHasDomainError",f"Unable to parse has_domain line '{line}'") - - ############################# - #### Process the has_regexp line - match = re.search("has_regexp",line) - if match: - match = re.search("^\s*relationship: has_regexp\s+(\S+)",line) - if match: - self.has_regexp = match.groups()[0] - has_match = True - else: - self.set_error("TermHasRegexpError",f"Unable to parse has_regexp line '{line}'") - - ############################# - #### Process the is_obsolete line - match = re.search("^\s*is_obsolete",line) - if match: - match = re.search("^\s*is_obsolete:\s*true\s*",line) - if match: - self.is_obsolete = True - has_match = True - else: - self.set_error("TermIsObsoleteError",f"Unable to parse is_obsolete line '{line}'") - - ############################# - #### Process the comment line - match = re.search("^\s*comment",line) - if match: - match = re.search("^\s*comment:\s*(.+)\s*",line) - if match: - self.comment = match.groups()[0] - has_match = True - else: - self.set_error("TermCommentError",f"Unable to parse comment line '{line}'") - - ############################# - #### Process the synonym line - match = re.search("^\s*synonym",line) - if match: - match = re.search('Japanese|Spanish',line) - if match: - continue - match = re.search('^\s*synonym:\s*"(.+)"\s*(\S+)\s*\[(.*)\].*$',line) - if match: - self.synonyms.append( { "type": match.groups()[1], "term": match.groups()[0], "origin": match.groups()[2] } ) - self.synonyms,match.groups()[0] - has_match = True - else: - match = re.search('^\s*synonym:\s*"(.+)"\s*(\S+)\s+(\S+)\s*\[(.*)\]\s*$',line) - if match: - self.synonyms.append( { "type": match.groups()[1], "term": match.groups()[0], "domain": match.groups()[2], "origin": match.groups()[3] } ) - self.synonyms,match.groups()[0] - has_match = True - else: - match = re.search('^\s*synonym:\s*"(.+)"\s*\[(.*)\]\s*$',line) - if match: - self.synonyms.append( { "type": 'unspecified', "term": match.groups()[0], "origin": match.groups()[1] } ) - self.synonyms,match.groups()[0] - has_match = True - else: - #self.set_error("TermSynonymError",f"Unable to parse synonym line '{line}'") - logging.error("TermSynonymError, Unable to parse synonym line '%s'", line) - has_match = True - - ############################# - #### Process the alt_id line - match = re.search("^\s*alt_id",line) - if match: - match = re.search('^\s*alt_id:\s*(\S+)\s*$',line) - if match: - pass - has_match = True - else: - self.set_error("TermAltIdError",f"Unable to parse alt_id line '{line}'") - - ############################# - #### Process the replaced_by line - match = re.search("^\s*replaced_by",line) - if match: - match = re.search('^\s*replaced_by:\s*(\S+)\s*$',line) - if match: - pass - has_match = True - else: - self.set_error("TermReplacedByError",f"Unable to parse replaced_by line '{line}'") - - ############################# - #### Process the property_value line - match = re.search("^\s*property_value",line) - if match: - match = re.search('^\s*property_value:\s*(.+)$',line) - if match: - pass - has_match = True - else: - self.set_error("TermPropertyValueError",f"Unable to parse property_value line '{line}'") - - ############################# - #### Process the other uninteresting lines - match = re.search("^\s*(consider|disjoint_from|intersection_of|created_by|creation_date|equivalent_to|union_of)",line) - if match: - pass - has_match = True - - ############################# - #### Process a namespace line - match = re.search("^namespace:",line) - if match: - match = re.search("^\s*namespace:\s*(.+)\s*$",line) - if match: - self.namespaces.append(match.groups()[0]) - has_match = True - else: - self.set_error("TermNamespaceError",f"Unable to parse namespeace line '{line}'") - - ############################# - #### Process a subset line - match = re.search("^subset:",line) - if match: - match = re.search("^\s*subset:\s*(.+)\s*$",line) - if match: - self.subsets.append(match.groups()[0]) - has_match = True - else: - self.set_error("TermSubsetError",f"Unable to parse subset line '{line}'") - - - #################################################################################### - #### Process mass modification data - - #### Parse xref: delta_mono_mass - match = re.search(r"^xref:\s*delta_mono_mass",line) - if has_match is False and match: - match = re.search(r'^xref:\s*delta_mono_mass\s+\"\s*([\+\-\.\d]+)\s*\"',line) - if match: - self.monoisotopic_mass = float(match.groups()[0]) - has_match = True - else: - self.set_error("TermDeltaMonoMassError",f"Unable to parse xref line '{line}'") - - #### Parse xref: delta_avge_mass - match = re.search(r"^xref:\s*delta_avge_mass",line) - if has_match is False and match: - match = re.search(r'^xref:\s*delta_avge_mass\s+\"\s*([\+\-\.\d]+)\s*\"',line) - if match: - self.average_mass = float(match.groups()[0]) - has_match = True - else: - self.set_error("TermDeltaAvgMassError",f"Unable to parse xref line '{line}'") - - #### Parse xref spec_NN_site - match = re.search(r"^xref:\s+spec_\d+_site",line) - if has_match is False and match: - match = re.search(r'^xref:\s+spec_\d+_site\s+\"\s*(.+)\s*\"',line) - if match: - self.sites[match.groups()[0]] = 1 - has_match = True - else: - self.set_error("TermSpecSiteError",f"Unable to parse xref line '{line}'") - - - ############################# - #### Process an other kind of xref line - match = re.search("^xref",line) - if has_match is False and match: - match = re.search("^\s*xref:\s+(\S+)\s*.*$",line) - if match: - self.xrefs.append(match.groups()[0]) - has_match = True - else: - self.set_error("TermXrefError",f"Unable to parse xref line '{line}'") - - ############################# - #### Process an other kind of relationship line - match = re.search("^relationship",line) - if has_match is False and match: - match = re.search("^\s*relationship: (.+)\s*$",line) - if match: - self.relationship_list.append(match.groups()[0]) - has_match = True - else: - self.set_error("TermRelationshipError",f"Unable to parse relationship line '{line}'") - - ############################# - #### If no match was found, add it to a pile of stuff we don't know how to deal with - if has_match is False: - self.unparsable_line_list.append(line) - - #### Set the is_valid state - if self.n_errors == 0: - self.is_valid = True - - else: - self.is_valid = False - logging.critical("Number of errors while parsing term '%s': %i", self.name, self.n_errors) - - if self.n_errors > 0 or len(self.unparsable_line_list) > 0: - print("=====================") - self.show() - sys.exit() - - - ######################################################################### - # Set the term to the error state - def set_error(self,error_code,error_message): - self.error_code = error_code - self.error_message = error_message - self.n_errors += 1 - logging.error("(%s): %s", error_code, error_message) - - - ######################################################################### - # Print out some information about the term - def show(self): - print(f"curie: {self.curie}") - print(f"is_valid: {self.is_valid}") - print(f"prefix: {self.prefix}") - print(f"identifier: {self.identifier}") - print(f"name: {self.name}") - print(f"definition: {self.definition}") - print(f"origin: {self.origin}") - print(f"value_type: {self.value_type}") - print(f"parents: {self.parents}") - print(f"children: {self.children}") - print(f"synonyms: {self.synonyms}") - print(f"has_units: {self.has_units}") - print(f"is_obsolete: {self.is_obsolete}") - - if self.monoisotopic_mass is not None: - print(f"=monoisotopic_mass: {self.monoisotopic_mass}") - print(f"=average_mass: {self.average_mass}") - print(f"=sites: {self.sites}") - - print(f"Number of unparsable lines: {len(self.unparsable_line_list)}") - if len(self.unparsable_line_list) > 0: - i_other_line = 0 - for line in self.unparsable_line_list: - print(" >"+line) - i_other_line += 1 - if i_other_line > 15: break - if i_other_line > 15: - print(" >...") - - - - -######################################################################### -#### A very simple example of using this class -def example(): - pass - - -######################################################################### -#### If class is run directly -def main(): - example() - -if __name__ == "__main__": main() diff --git a/implementations/python/mzlib/peak_list.py b/implementations/python/mzlib/peak_list.py deleted file mode 100644 index e0411f2..0000000 --- a/implementations/python/mzlib/peak_list.py +++ /dev/null @@ -1,100 +0,0 @@ -import enum - -from pprint import pformat -from numbers import Number -from typing import List, Union, Mapping, Sequence, Iterator - -import numpy as np - -PeakDtype = np.dtype([('mz', np.float64), ('intensity', np.float32), - ('annotation', object), ('aggregation', object)]) - -PeakType = Mapping[str, Union[float, list]] - -class ErrorUnit(enum.Enum): - Da = 'da' - PPM = 'ppm' - - -class PeakList(Sequence[PeakType]): - peaks: np.ndarray - - def __init__(self, peaks): - if isinstance(peaks, np.ndarray) and peaks.dtype == PeakDtype: - self.peaks = peaks - else: - self.peaks = np.array([tuple(p) for p in peaks], dtype=PeakDtype) - - def __len__(self): - return len(self.peaks) - - def __getitem__(self, i): - return self.peaks[i] - - def __iter__(self) -> Iterator[PeakType]: - return iter(self.peaks) - - def __repr__(self): - return f"{self.__class__.__name__}({pformat(self.peaks, indent=2)})" - - def __eq__(self, other): - if other is None: - return False - if not isinstance(other, PeakList): - other = PeakList(other) - valid = np.allclose(self.peaks['mz'], other.peaks['mz']) - if not valid: - return False - valid = np.allclose(self.peaks['intensity'], other.peaks['intensity']) - if not valid: - return False - return True - - def __ne__(self, other): - return not self == other - - def find(self, mz, error_tolerance=10, error_unit='ppm') -> List[Sequence[PeakType]]: - if isinstance(mz, Number): - mz = [mz] - mzs = self.peaks['mz'] - ii = np.searchsorted(mzs, mz) - n = len(self) - error_unit = ErrorUnit(error_unit) - - outs = [] - if error_unit == ErrorUnit.Da: - for i, mz_i in zip(ii, mz): - low = i - 1 - while low >= 0: - if abs(mzs[low] - mz_i) < error_tolerance: - low -= 1 - else: - low += 1 - break - high = i - while high < n: - if abs(mzs[high] - mz_i) < error_tolerance: - high += 1 - else: - high -= 1 - break - outs.extend(self.peaks[slice(low, high + 1)]) - elif error_unit == ErrorUnit.PPM: - error_tolerance /= 1e6 - for i, mz_i in zip(ii, mz): - low = i - 1 - while low >= 0: - if abs(mzs[low] - mz_i) / mz_i < error_tolerance: - low -= 1 - else: - low += 1 - break - high = i - while high < n: - if abs(mzs[high] - mz_i) / mz_i < error_tolerance: - high += 1 - else: - high -= 1 - break - outs.extend(self.peaks[slice(low, high + 1)]) - return outs diff --git a/implementations/python/mzlib/spectrum.py b/implementations/python/mzlib/spectrum.py deleted file mode 100644 index 316d717..0000000 --- a/implementations/python/mzlib/spectrum.py +++ /dev/null @@ -1,229 +0,0 @@ -from __future__ import print_function - -import textwrap - -from typing import Any, Dict, List, Optional, TYPE_CHECKING - -from mzlib.attributes import ( - AttributeManager, AttributeManagedProperty, AttributeListManagedProperty, - AttributeProxy as _AttributeProxy, AttributeFacet -) -from mzlib.analyte import Analyte, InterpretationCollection, Interpretation - -if TYPE_CHECKING: - from mzlib.spectrum_library import SpectrumLibrary - -#A class that holds data for each spectrum that is read from the SpectralLibrary class - -SPECTRUM_NAME = "MS:1003061|library spectrum name" -LIBRARY_SPECTRUM_KEY = "MS:1003237|library spectrum key" -LIBRARY_SPECTRUM_INDEX = "MS:1003062|library spectrum index" -PRECURSOR_MZ = "MS:1003208|experimental precursor monoisotopic m/z" -CHARGE_STATE = "MS:1000041|charge state" - - -class SpectrumAggregation(_AttributeProxy): - aggregation_type = AttributeManagedProperty("MS:1003065|spectrum aggregation type") - replicates_used = AttributeManagedProperty[int]("MS:1003070|number of replicate spectra used") - replicates_available = AttributeManagedProperty[int]("MS:1003069|number of replicate spectra available") - - -class Spectrum(AttributeManager): - peak_list: List - analytes: Dict[str, Analyte] - interpretations: InterpretationCollection - _source: Optional['SpectrumLibrary'] - - #### Constructor - def __init__(self, attributes=None, peak_list=None, analytes=None, - interpretations=None): - """ - - Parameters - ---------- - attributes : list - A list of attribute [key, value (, group)] sets to initialize to. - peak_list : list - A list of tuples representing (annotated) peaks - analytes : dict[str, :class:`~.Analyte`] - A mapping from identifier to :class:`~.Analyte` unique within this - :class:`Spectrum`. - interpretations : :class:`~.InterpretationCollection` - A mapping from identifier to :class:`~.Interpretation` unique within - this :class:`Spectrum`. - """ - if peak_list is None: - peak_list = [] - if analytes is None: - analytes = dict() - if interpretations is None: - interpretations = InterpretationCollection() - else: - interpretations = InterpretationCollection(interpretations) - super(Spectrum, self).__init__(attributes) - self.peak_list = peak_list - self.analytes = analytes - self.interpretations = interpretations - - name = AttributeManagedProperty[str](SPECTRUM_NAME) - key = AttributeManagedProperty[int](LIBRARY_SPECTRUM_KEY) - index = AttributeManagedProperty[int](LIBRARY_SPECTRUM_INDEX) - - precursor_mz = AttributeListManagedProperty[float]( - [PRECURSOR_MZ, - "MS:1003053|theoretical monoisotopic m/z"]) - - _precursor_charge = AttributeManagedProperty[int](CHARGE_STATE) - - spectrum_aggregation = AttributeFacet[SpectrumAggregation](SpectrumAggregation) - peak_aggregations = AttributeManagedProperty("MS:1003254|peak attribute", multiple=True) - - @property - def precursor_charge(self) -> int: - if self._precursor_charge: - self._precursor_charge - for analyte in self.analytes.values(): - if analyte.charge: - return analyte.charge - - def add_analyte(self, analyte: Analyte): - self.analytes[str(analyte.id)] = analyte - - def get_analyte(self, analyte_id: str) -> Analyte: - return self.analytes[str(analyte_id)] - - def remove_analyte(self, analyte_id: str): - analyte_id = str(analyte_id) - del self.analytes[analyte_id] - interpretation: Interpretation - for interpretation in self.interpretations.values(): - if interpretation.has_analyte(analyte_id): - interpretation.remove_analyte(analyte_id) - - def add_interpretation(self, interpretation: Interpretation): - self.interpretations.add_interpretation(interpretation) - - def get_interpretation(self, interpretation_id: str) -> Interpretation: - return self.interpretations.get_interpretation(interpretation_id) - - def __eq__(self, other): - result = super(Spectrum, self).__eq__(other) - if result: - result = self.peak_list == other.peak_list - if result: - result = self.analytes == other.analytes - return result - - def __repr__(self): # pragma: no cover - template = f"{self.__class__.__name__}(" - lines = list(map(str, self.attributes)) - if not lines: - template += "[], " - else: - template += "[\n%s], " % textwrap.indent(',\n'.join(lines), ' ' * 2) - lines = list(map(str, self.peak_list)) - if not lines: - template += "peak_list=[])" - else: - template += "peak_list=[\n%s])" % textwrap.indent( - ',\n'.join(lines), ' ' * 2) - return template - - def __str__(self): # pragma: no cover - return self.write("text") - - def write(self, format="text", **kwargs): # pragma: no cover - """ - Write out the spectrum in any of the supported formats - - Parameters - ---------- - format : str - The name of the format to write in - **kwargs - Passed to implementation - """ - #### Set a buffer to fill with string data - buffer = '' - - #### Make the format string lower case to facilitate comparisons - format = format.lower() - - #### If the format is text - if format == "text": - from mzlib.backends.text import format_spectrum - return format_spectrum(self, **kwargs) - - #### If the format is TSV - elif format == "tsv" or format == "csv": - - #### Set the appropriate delimiter for format - delimiter = "\t" - if format == "csv": - delimiter = "," - - #### Create the header line and columns line - buffer += "# Spectrum attributes\n" - buffer += delimiter.join("cv_param_group", "accession", "name", "value_accession", "value\n") - - for attribute in self.attributes: - if len(attribute) == 2: - key,value = attribute - cv_param_group = '' - elif len(attribute) == 3: - key,value,cv_param_group = attribute - if format == "csv" and ',' in str(value): - value = '"' + value + '"' - else: - print("ERROR: Unsupported number of items in attribute") - print(attribute) - raise ValueError( - f"Unsupported number of items in attribute: {attribute}") - components = key.split('|',1) - if len(components) == 2: - accession,name = components - else: - print("ERROR: Unsupported number of items in components") - print(components) - raise ValueError(f"Unsupported number of items in components: {components}") - components = str(value).split('|',1) - if len(components) == 2: - value_accession,value = components - value = str(value) - if format == "csv" and ',' in value: - value = '"' + value + '"' - elif len(components) == 1: - value = str(value) - if format == "csv" and ',' in value: - value = '"' + value + '"' - value_accession = '' - else: - print("ERROR: Unsupported number of items in components") - print(components) - raise ValueError( - f"Unsupported number of items in components: {components}") - - #### Create the data line - buffer += delimiter.join(map(str, [cv_param_group,accession,name,value_accession,value]))+"\n" - - #### Create the header line and columns line - buffer += "# Peak list\n" - buffer += "mz\tintensity\tinterpretation\n" - - #### Write out the peak list - for peak in self.peak_list: - mz,intensity,interpretation = peak - if format == "csv" and ',' in str(interpretation): - interpretation = '"' + interpretation + '"' - buffer += delimiter.join(map(str, [mz,intensity,interpretation]))+"\n" - - #### If the format is JSON - elif format == "json": - from mzlib.backends.json import format_spectrum - return format_spectrum(self, **kwargs) - - #### Otherwise we don't know this format - else: - raise ValueError(f"ERROR: Unrecogized format '{format}'") - - return(buffer) diff --git a/implementations/python/mzlib/spectrum_library.py b/implementations/python/mzlib/spectrum_library.py deleted file mode 100644 index bd1b0ff..0000000 --- a/implementations/python/mzlib/spectrum_library.py +++ /dev/null @@ -1,391 +0,0 @@ -#!/usr/bin/env python3 -import os -import pathlib - -from typing import Optional, Type, List, Union -from mzlib.attributes import AttributeManagedProperty -from mzlib.backends.base import LIBRARY_DESCRIPTION_TERM, LIBRARY_NAME_TERM, LIBRARY_URI_TERM, LIBRARY_VERSION_TERM -from mzlib.cluster import SpectrumCluster - -from mzlib.spectrum_library_index import SpectrumLibraryIndex -from mzlib.spectrum import Spectrum -from mzlib.index import IndexBase -from mzlib.backends import guess_implementation, SpectralLibraryBackendBase, SpectralLibraryWriterBase - - -debug = False - -class SpectrumLibrary: - """ - SpectrumLibrary - Class for a spectrum library - - Attributes - ---------- - identifier: str - A unique identifier string assigned to this library by a spectral library host or - provider. - filename: str or Path - A location on the local file system where the spectral library is stored - format : str - The name of the format for the current encoding of the library. - backend: :class:`~.SpectralLibraryBackendBase` - The implementation used to parse the file - - Methods - ------- - read_header - Read just the header of the whole library - read - Read the entire library into memory - write - Write the library to disk - create_index - Create an index file for this library - transform - Not quite sure what this is supposed to be - get_spectrum - Extract a single spectrum by identifier - find_spectra - Return a list of spectra given query constraints - - """ - - backend: SpectralLibraryBackendBase - filename: str - identifier: str - format: str - index_type: Type[IndexBase] - - name = AttributeManagedProperty[str](LIBRARY_NAME_TERM) - description = AttributeManagedProperty[str](LIBRARY_DESCRIPTION_TERM) - uri = AttributeManagedProperty[str](LIBRARY_URI_TERM) - library_version = AttributeManagedProperty[str](LIBRARY_VERSION_TERM) - - def __init__(self, identifier=None, filename=None, format=None, index_type=None): - """ - __init__ - SpectrumLibrary constructor - - Parameters - ---------- - identifier : str, optional - A universal identifier for a hosted spectral library to fetch. - filename : str, os.PathLike, or io.IOBase, optional - A path-like or file-like object that holds a spectral library to read. - format : string - Name of the format for the current encoding of the library. - index_type : Type[:class:`~.mzlib.index.base.IndexBase`] - The type of index to preferentially construct. - """ - self.backend = None - self.identifier = identifier - self.index_type = index_type - self._format = format - self.filename = filename - - def _init_from_filename(self, index_type: Type[IndexBase]=None): - if index_type is None: - index_type = self.index_type - if self.format is None: - self.backend = guess_implementation(self.filename, index_type) - self._format = self.backend.format_name - else: - if callable(self.format): - backend_type = self.format - else: - backend_type = SpectralLibraryBackendBase.type_for_format(self.format) - if backend_type is None: - raise ValueError( - f"Could not find an implementation for {self.format}") - self.backend = backend_type( - self.filename, index_type=index_type) - self._format = self.backend.format_name - self._identifier = self.backend.identifier - - def _backend_initialized(self): - return self.backend is not None - - def _requires_backend(self): - if not self._backend_initialized(): - raise ValueError( - "Cannot read library data, library parser not yet initialized") - - @property - def spectrum_attribute_sets(self): - self._requires_backend() - return self.backend.spectrum_attribute_sets - - @property - def analyte_attribute_sets(self): - self._requires_backend() - return self.backend.analyte_attribute_sets - - @property - def interpretation_attribute_sets(self): - self._requires_backend() - return self.backend.interpretation_attribute_sets - - @property - def cluster_attribute_sets(self): - self._requires_backend() - return self.backend.cluster_attribute_sets - - #### Define getter/setter for attribute identifier - @property - def identifier(self) -> Optional[str]: - if self._identifier is None: - if self._backend_initialized(): - return self.backend.identifier - return self._identifier - - @identifier.setter - def identifier(self, identifier: Optional[str]): - self._identifier = identifier - if self.backend is not None: - self.backend.identifier = identifier - - #### Define getter/setter for attribute filename - @property - def filename(self): - return(self._filename) - - @filename.setter - def filename(self, filename): - self._filename = filename - if filename is not None: - self._init_from_filename() - - #### Define getter/setter for attribute format - @property - def format(self): - return self._format - - @property - def index(self): - if self._backend_initialized(): - return self.backend.index - return None - - @property - def attributes(self): - if self._backend_initialized(): - return self.backend.attributes - return None - - def read_header(self) -> bool: - """ - Read just the header of the whole library - - Returns - ------- - bool: - Whether the operation was successful - """ - self._requires_backend() - return self.backend.read_header() - - def read(self): - """ - Create a sequential iterator over the spectrum library entries. - - Yields - ------ - Spectrum or SpectrumCluster - """ - self._requires_backend() - return self.backend.read() - - def write(self, destination, format: str=None, **kwargs): - """ - Write the library to disk. - - Parameters - ---------- - destination : str, os.PathLike, or io.IOBase - The path or stream to write the library to. - format : str, Type, or Callable - The name of the format or a callable object that returns - a :class:`~.SpectrumLibraryWriterBase`. - **kwargs - Passed to implementation. - """ - filename = destination - if not isinstance(filename, (str, pathlib.Path, os.PathLike)): - filename = getattr(destination, "name", None) - - if format is None and filename is not None: - basename = os.path.basename(filename) - tokens = basename.rsplit(".", 2) - if len(tokens) == 3: - writer_type = SpectralLibraryWriterBase.type_for_format('.'.join(tokens[1:])) - else: - raise ValueError(f"Could not guess format from file name {filename}") - else: - writer_type = SpectralLibraryWriterBase.type_for_format(format) - if writer_type is None: - raise ValueError( - f"Could not find a format writer from file name {filename} or format {format}") - writer = writer_type(destination, **kwargs) - if self._backend_initialized(): - with writer: - writer.write_library(self.backend) - else: - print("Library not initialized") - writer.close() - - def get_spectrum(self, spectrum_number: int=None, spectrum_name: str=None) -> Spectrum: - """ - Retrieve a single spectrum from the library. - - Parameters - ---------- - spectrum_number : int, optional - The index of the specturm in the library - spectrum_name : str, optional - The name of the spectrum in the library - - Returns - ------- - :class:`~.Spectrum` - """ - self._requires_backend() - return self.backend.get_spectrum(spectrum_number, spectrum_name) - - def get_cluster(self, cluster_number: int) -> SpectrumCluster: - """ - Retrieve a single spectrum cluster from the library. - - Parameters - ---------- - cluster_number : int, optional - The index of the cluster in the library - - Returns - ------- - :class:`~.SpectrumCluster` - """ - self._requires_backend() - return self.backend.get_cluster(cluster_number) - - def find_spectra(self, specification, **query_keys) -> List[Spectrum]: - """ - Return a list of spectra given query constraints - - Returns - ------- - List[Spectrum] - """ - self._requires_backend() - return self.backend.find_spectra(specification, **query_keys) - - def __getitem__(self, i: int) -> Spectrum: - self._requires_backend() - return self.backend[i] - - def __len__(self): - if self._backend_initialized(): - return len(self.backend) - return 0 - - def __iter__(self): - if self._backend_initialized(): - return iter(self.backend) - return iter([]) - - def add_attribute(self, key, value, group_identifier=None): - """ - Add an attribute to the library level attributes store. - - Parameters - ---------- - key : str - The name of the attribute to add - value : object - The value of the attribute to add - group_identifier : str, optional - The attribute group identifier to use, if any. If not provided, - no group is assumed. - """ - self._requires_backend() - return self.backend.add_attribute(key, value, group_identifier=group_identifier) - - def get_attribute(self, key, group_identifier=None): - """ - Get the value or values associated with a given - attribute key from the library level attribute store. - - Parameters - ---------- - key : str - The name of the attribute to retrieve - group_identifier : str, optional - The specific group identifier to return from. - - Returns - ------- - attribute_value: object or list[object] - Returns single or multiple values for the requested attribute. - """ - self._requires_backend() - return self.backend.get_attribute(key, group_identifier=group_identifier) - - def remove_attribute(self, key, group_identifier=None): - """ - Remove the value or values associated with a given - attribute key from the library level attribute store. - - This rebuilds the entire store, which may be expensive. - - Parameters - ---------- - key : str - The name of the attribute to retrieve - group_identifier : str, optional - The specific group identifier to return from. - - """ - self._requires_backend() - return self.backend.remove_attribute(key, group_identifier=group_identifier) - - def has_attribute(self, key): - """ - Test for the presence of a given attribute in the library - level store. - - Parameters - ---------- - key : str - The attribute to test for - - Returns - ------- - bool - """ - self._requires_backend() - return self.backend.has_attribute(key) - - def summarize_parsing_errors(self): - return self.backend.summarize_parsing_errors() - - - -#### Example using this class -def example(): - - #### Create a new RTXFeedback object - spectrum_library = SpectrumLibrary() - spectrum_library.filename = "../refData/sigmaups1_consensus_final_true_lib.msp" - spectrum_library.read_header() - - spectrum_buffer = spectrum_library.get_spectrum(spectrum_index_number=2000) - spectrum = Spectrum() - spectrum.parse(spectrum_buffer) - buffer = spectrum.write(format="text") - print(buffer) - print() - - return() - - -#### If this class is run from the command line, perform a short little test to see if it is working correctly -def main(): - - #### Run an example - example() - return() - - -if __name__ == "__main__": main() - diff --git a/implementations/python/mzlib/spectrum_library_collection.py b/implementations/python/mzlib/spectrum_library_collection.py deleted file mode 100644 index d6541aa..0000000 --- a/implementations/python/mzlib/spectrum_library_collection.py +++ /dev/null @@ -1,381 +0,0 @@ -#!/usr/bin/env python3 -# pragma: no cover -from __future__ import print_function -import sys -def eprint(*args, **kwargs): - print(*args, file=sys.stderr, **kwargs) - -import os -from datetime import datetime - -from sqlalchemy import Column, ForeignKey, Integer, Float, String, DateTime, Text, PickleType, LargeBinary -from sqlalchemy.ext.declarative import declarative_base -from sqlalchemy.orm import relationship -from sqlalchemy import create_engine -from sqlalchemy.orm import sessionmaker -from sqlalchemy import desc -from sqlalchemy import inspect - -Base = declarative_base() - -debug = False - -#### Define the database tables as classes -class LibraryRecord(Base): - __tablename__ = 'library_record' - library_record_id = Column(Integer, primary_key=True) - id_name = Column(String(255), nullable=False) - version = Column(String(255), nullable=False) - status = Column(String(255), nullable=False) - original_name = Column(String(255), nullable=False) - original_checksum = Column(String(255), nullable=True) - n_entries = Column(Integer, nullable=True) - record_datetime = Column(DateTime, nullable=False) - - -class SpectrumLibraryCollection: - """ - SpectrumLibraryCollection - Class for a collection of spectrum libraries - - Attributes - ---------- - filename : string - Filename of the SQLite database file that contains information about the collection of libraries available. - - Methods - ------- - create - Create a new spectral library collection - show - Return a string that summarizes the state of the collection - get_libraries - Return a list of available libraries - get_library - Return attributes of a specific library - add_library - Add a new library - create_index - Create a master index from all the constituent library indexes to be able to find spectra in any library - find_spectra - Return a list of spectra given query constraints - - """ - - - def __init__(self, filename=None): - """ - __init__ - SpectrumLibraryCollection constructor - - Parameters - ---------- - filename : string - Filename of the SQLite database file that contains information about the collection of libraries available. - - """ - - self.filename = filename - if os.path.exists(self.filename): - if debug: eprint(f"INFO: Library collection {self.filename} exists") - self.connect() - else: - if debug: eprint(f"INFO: Library collection {self.filename} not found. Will create new.") - self.createDatabase() - - - #### Destructor - def __del__(self): - self.disconnect() - - - #### Define getter/setter for attribute filename - @property - def filename(self): - return(self._filename) - @filename.setter - def filename(self, filename): - self._filename = filename - - - #### Define attribute session - @property - def session(self) -> str: - return self._session - - @session.setter - def session(self, session: str): - self._session = session - - - #### Define attribute engine - @property - def engine(self) -> str: - return self._engine - - @engine.setter - def engine(self, engine: str): - self._engine = engine - - - #### Delete and create the database. Careful! - def createDatabase(self): - if os.path.exists(self.filename): - eprint("INFO: Deleting previous database file " + self.filename) - os.remove(self.filename) - if debug: eprint("INFO: Creating database " + self.filename) - engine = create_engine("sqlite:///"+self.filename) - Base.metadata.create_all(engine) - self.connect() - - - #### Create and store a database connection - def connect(self): - if debug: eprint("INFO: Connecting to database " + self.filename) - engine = create_engine("sqlite:///"+self.filename) - DBSession = sessionmaker(bind=engine) - session = DBSession() - self.session = session - self.engine = engine - - - #### Destroy the database connection - def disconnect(self): - if debug: eprint("INFO: Disconnecting from database " + self.filename) - session = self.session - engine = self.engine - session.close() - engine.dispose() - - - def create(self, overwrite_existing=False): - """ - create - Create a new spectral library collection - - Extended description of function. - - Parameters - ---------- - overwrite_existing : boolean - Set to true in order to write over the previous file if it exists - - Returns - ------- - int - Description of return value - """ - - #### Begin functionality here - if debug: eprint("INFO: Creating database " + self.filename) - if os.path.exists(self.filename): - os.remove(self.filename) - engine = create_engine("sqlite:///"+self.filename) - Base.metadata.create_all(engine) - self.connect() - return() - - - def get_libraries(self): - """ - get_libraries - Return a list of available libraries - - Extended description of function. - - Parameters - ---------- - - Returns - ------- - int - Description of return value - """ - - #### Begin functionality here - if debug: eprint("INFO: Fetching all libraries") - session = self.session - libraries = session.query(LibraryRecord).all() - return(libraries) - - - def get_library(self,identifier=None,version=None,filename=None): - """ - get_library - Return attributes of a specific library - - Extended description of function. - - Parameters - ---------- - - Returns - ------- - int - Description of return value - """ - - session = self.session - if identifier is not None and identifier > "": - libraries = session.query(LibraryRecord).filter(LibraryRecord.id_name==identifier).order_by(desc(LibraryRecord.version)).all() - if len(libraries) == 0: - raise Exception(f"No library with identifier {identifier} found") - else: - libraryListStr = "" - for library in libraries: - libraryListStr += library.version+"," - if version is not None and version > "": - if version == library.version: - return(library) - if version is not None and version > "": - raise Exception(f"Unable to find version {version} of library {identifier}") - if len(libraries) == 1: - return(library) - raise Exception(f"There are several version of this library ({libraryListStr}). Please specify a version") - return() - - elif filename is not None and filename > "": - raise Exception("Search by filename not implemented") - else: - raise Exception("Not enough information to find library") - - return() - - - def add_library(self, original_name, version="1"): - """ - add_library - Add a new library - - Extended description of function. - - Parameters - ---------- - - Returns - ------- - int - Description of return value - """ - - #### Begin functionality here - if debug: eprint("INFO: Adding a library entry") - session = self.session - library_record = LibraryRecord(id_name="PXL000000", version=version, - status="initial_add",original_name=original_name,record_datetime=datetime.now()) - session.add(library_record) - session.flush() - assert(library_record.library_record_id) - idstr = str(library_record.library_record_id) - if debug: eprint(f"INFO: Returned id={idstr}") - idstr_length = len(idstr) - assert(idstr_length) - padding = "000000" - new_idstr = "PXL" + padding[0:len(padding)-idstr_length] + idstr - library_record.id_name = new_idstr - session.flush() - session.commit() - return() - - - def update_library_metadata(self, id, version=None): - """ - update_library_metadata - Update the metadata associated with a library - - Extended description of function. - - Parameters - ---------- - - Returns - ------- - int - Description of return value - """ - - #### Begin functionality here - if debug: eprint(f"INFO: Updating the library entry with id {id}") - session = self.session - library = session.query(LibraryRecord).filter(LibraryRecord.library_record_id==id).first() - if library is not None: - if version is not None: - print(f" Updating version to {version}") - library.version = version - session.flush() - session.commit() - else: - print(f"ERROR: Library entry with id {id} not found") - - - def create_index(self): - """ - create_index - Create a master index from all the constituent library indexes to be able to find spectra in any library - - Extended description of function. - - Parameters - ---------- - - Returns - ------- - int - Description of return value - """ - - #### Begin functionality here - - return() - - - def find_spectra(self): - """ - find_spectra - Return a list of spectra given query constraints - - Extended description of function. - - Parameters - ---------- - - Returns - ------- - int - Description of return value - """ - - #### Begin functionality here - - return() - - -#### Example using this class -def example(): - - #### Create a new or attach to existing library collection - spec_lib_collection = SpectrumLibraryCollection("zzTest.sqlite") - - #### Add a library - spec_lib_collection.add_library() - - #### Show all libraries - libraries = spec_lib_collection.get_libraries() - if ( libraries is None ): - print("The library collection is empty") - else: - for library in libraries: - print(library.library_record_id,library.id_name,library.original_name) - - return() - - -#### Example using this class -def example2(): - - #### Create a new or attach to existing library collection - spec_lib_collection = SpectrumLibraryCollection("../spectralLibraries/SpectrumLibraryCollection.sqlite") - - try: - library = spec_lib_collection.get_library(identifier="PXL000003", version="05-24-2011") - except Exception as error: - print("ERROR:",error) - return() - print("\t".join([str(library.library_record_id),library.id_name,library.version,library.original_name])) - return() - - -#### If this class is run from the command line, perform a short little test to see if it is working correctly -def main(): - - #### Run an example - example2() - return() - - -if __name__ == "__main__": main() - diff --git a/implementations/python/mzlib/spectrum_library_index.py b/implementations/python/mzlib/spectrum_library_index.py deleted file mode 100644 index 665b95a..0000000 --- a/implementations/python/mzlib/spectrum_library_index.py +++ /dev/null @@ -1,357 +0,0 @@ -#!/usr/bin/env python3 - -# pragma: no cover -from __future__ import print_function -import sys -def eprint(*args, **kwargs): - print(*args, file=sys.stderr, **kwargs) - -import os -from datetime import datetime - -from sqlalchemy import Column, ForeignKey, Integer, Float, String, DateTime, Text, PickleType, LargeBinary -from sqlalchemy.ext.declarative import declarative_base -from sqlalchemy.orm import relationship -from sqlalchemy import create_engine -from sqlalchemy.orm import sessionmaker -from sqlalchemy import desc -from sqlalchemy import inspect - -Base = declarative_base() - -debug = False - - -#### Define the database tables as classes -class SpectrumLibraryIndexAttribute(Base): - __tablename__ = 'spectrum_library_index_attribute' - id = Column(Integer, primary_key=True) - name = Column(String(255), nullable=False) - value = Column(String(1024), nullable=False) - - -#### Define the database tables as classes -class SpectrumLibraryIndexRecord(Base): - __tablename__ = 'spectrum_library_index_record' - id = Column(Integer, primary_key=True) - number = Column(Integer, nullable=False) - offset = Column(Integer, nullable=False) - name = Column(String(1024), nullable=False) - peptide_sequence = Column(String(2014), nullable=True) - - -class SpectrumLibraryIndex: - """ - SpectrumLibraryIndex - Class for a spectrum library index - - Attributes - ---------- - columns : array - Names of the columns in the data matrix - - Methods - ------- - get_offset - Get the offset for a spectrum in the library based on the spectrum_index or spectrum_name - find_offsets - Return an array of offsets of spectra that match the input parameters - create_index - Create a new index for a library - add_spectrum - Add a spectrum to the index - - """ - - - #### Constructor - def __init__(self, library_filename=None, version=None, n_spectra=None, library_datetime=None, columns=None): - """ - __init__ - SpectrumLibraryIndex constructor - - Parameters - ---------- - columns : array - Names of the columns in the data matrix - - """ - - self.library_filename = library_filename - self.version = "0.1" - self.n_spectra = 0 - self.library_datetime = None - self.columns = [ 'number', 'offset', 'name', 'peptide_sequence' ] - self.status = 'closed' - self.uncommitted_transactions = 0 - - if library_filename is None: - raise Exception('Library filename missing') - filename = self.library_filename + '.splindex' - if filename is None: - raise Exception('Missing library_filename') - if os.path.exists(filename): - self.connect() - self.status = 'OK' - else: - self.create_database() - self.status = 'OK' - - - #### Destructor - def __del__(self): - if self.library_filename is not None: - self.disconnect() - - - #### Define getter/setter for attribute library_filename - @property - def library_filename(self): - return(self._library_filename) - @library_filename.setter - def library_filename(self, library_filename): - self._library_filename = library_filename - - #### Define getter/setter for attribute version - @property - def version(self): - return(self._version) - @version.setter - def version(self, version): - self._version = version - - #### Define getter/setter for attribute n_spectra - @property - def n_spectra(self): - return(self._n_spectra) - @n_spectra.setter - def n_spectra(self, n_spectra): - self._n_spectra = n_spectra - - #### Define getter/setter for attribute library_datetime - @property - def library_datetime(self): - return(self._library_datetime) - @library_datetime.setter - def library_datetime(self, library_datetime): - self._library_datetime = library_datetime - - #### Define getter/setter for attribute columns - @property - def columns(self): - return(self._columns) - @columns.setter - def columns(self, columns): - self._columns = columns - - - #### Define attribute session - @property - def session(self) -> str: - return self._session - - @session.setter - def session(self, session: str): - self._session = session - - - #### Define attribute engine - @property - def engine(self) -> str: - return self._engine - - @engine.setter - def engine(self, engine: str): - self._engine = engine - - - #### Delete and create the database. Careful! - def create_database(self): - filename = self.library_filename + '.splindex' - if os.path.exists(filename): - if debug: eprint(f'INFO: Deleting previous index file {filename}') - os.remove(filename) - if debug: eprint(f'INFO: Creating index file {filename}') - engine = create_engine("sqlite:///"+filename) - Base.metadata.create_all(engine) - - DBSession = sessionmaker(bind=engine) - session = DBSession() - self.session = session - self.engine = engine - - index_attribute = SpectrumLibraryIndexAttribute( name='version', value=self.version ) - session.add(index_attribute) - index_attribute = SpectrumLibraryIndexAttribute( name='n_spectra', value=0 ) - session.add(index_attribute) - - session.flush() - session.commit() - - - #### Create and store a database connection - def connect(self): - filename = self.library_filename + '.splindex' - if debug: eprint(f'INFO: Opening index file {filename}') - engine = create_engine("sqlite:///"+filename) - DBSession = sessionmaker(bind=engine) - session = DBSession() - self.session = session - self.engine = engine - - - #### Destroy the database connection - def disconnect(self): - filename = self.library_filename + '.splindex' - if self.uncommitted_transactions > 0: - if debug: eprint(f'INFO: Committing open transactions') - self.session.flush() - self.session.commit() - self.uncommitted_transactions = 0 - - if debug: eprint(f'INFO: Closing index file {filename}') - session = self.session - engine = self.engine - session.close() - engine.dispose() - self.session = None - self.engine = None - - - #### Destroy the database connection - def commit(self): - if self.uncommitted_transactions > 0: - #if debug: eprint(f'INFO: Committing open transactions') - self.session.flush() - self.session.commit() - self.uncommitted_transactions = 0 - - - def get_offset(self, spectrum_index_number=None, spectrum_name=None): - """ - get_offset - Get the offset for a spectrum in the library based on the spectrum_index or spectrum_name - - Extended description of function. - - Parameters - ---------- - spectrum_index : integer - Index number of the spectrum to select - spectrum_name : string - Name of the spectrum to select - - Returns - ------- - int - Description of return value - """ - - #### Begin functionality here - #TODO: Check if SpectrumLibrary is empty or not yet indexed. - if spectrum_index_number is not None: - try: - records = self.session.query(SpectrumLibraryIndexRecord).filter(SpectrumLibraryIndexRecord.number==spectrum_index_number).all() - except: - self.session.rollback() - raise - if len(records) > 1: - raise Exception('Too many records') - return(records[0].offset) - - return() - - - def find_offsets(self): - """ - find_offsets - Return an array of offsets of spectra that match the input parameters - - Extended description of function. - - Parameters - ---------- - - Returns - ------- - int - Description of return value - """ - - #### Begin functionality here - - return() - - - def create_index(self): - """ - create_index - Create a new index for a library - - Extended description of function. - - Parameters - ---------- - - Returns - ------- - int - Description of return value - """ - - #### Begin functionality here - if self.session is not None: - self.disconnect() - self.create_database() - return(True) - - - def add_spectrum(self, number=None, offset=None, name=None, peptide_sequence=None): - """ - add_spectrum - Add a spectrum to the index - - Extended description of function. - - Parameters - ---------- - number : integer - Index number of the spectrum to add - offset : integer - File offset of the spectrum to add - name : string - Name of the spectrum to add - peptide_sequence : string - Unmodified peptide sequence of the spectrum to add - - Returns - ------- - int - Description of return value - """ - - #### Begin functionality here - #if debug: eprint("INFO: Adding an index entry") - session = self.session - index_record = SpectrumLibraryIndexRecord( number=number, offset=offset, name=name, peptide_sequence=peptide_sequence ) - session.add(index_record) - self.uncommitted_transactions += 1 - if self.uncommitted_transactions >= 5000: - session.flush() - session.commit() - self.uncommitted_transactions = 0 - - self.status = 'uncommitted changes' - return() - - - -#### Example using this class -def example(): - - #### Create a new RTXFeedback object - index = SpectrumLibraryIndex(library_filename='../refData/sigmaups1_consensus_final_true_lib.msp') - print(index.version) - return() - - -#### If this class is run from the command line, perform a short little test to see if it is working correctly -def main(): - - #### Run an example - example() - return() - - -if __name__ == "__main__": main() - diff --git a/implementations/python/mzlib/tools/__init__.py b/implementations/python/mzlib/tools/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/implementations/python/mzlib/tools/cli.py b/implementations/python/mzlib/tools/cli.py deleted file mode 100644 index 7c3abcd..0000000 --- a/implementations/python/mzlib/tools/cli.py +++ /dev/null @@ -1,211 +0,0 @@ -import logging -import sys -import click -import logging -import json -import csv - -from typing import DefaultDict, List - -from mzlib.spectrum_library import SpectrumLibrary -from mzlib.index import MemoryIndex, SQLIndex -from mzlib.backends.base import FormatInferenceFailure, SpectralLibraryBackendBase -from mzlib.validate import validator -from mzlib.validate.level import RequirementLevel -from mzlib.ontology import ControlledVocabularyResolver - -from mzlib.tools.utils import ColoringFormatter - -CONTEXT_SETTINGS = dict(help_option_names=['-h', '--help']) - -logger = logging.getLogger(__name__) - - -def _display_tree(tree, indent: int=0): - if isinstance(tree, dict): - if not tree: - return - for k, v in tree.items(): - if isinstance(v, (list, dict)) and not v: - continue - click.echo(f"{' ' * indent}└-{k}", err=True, nl=True) - _display_tree(v, indent + 2) - elif isinstance(tree, list): - for v in tree: - _display_tree(v, indent + 2) - else: - click.echo(f"{' ' * indent}└-{tree}", err=True, nl=True) - - -@click.group(context_settings=CONTEXT_SETTINGS) -def main(): - """A collection of utilities for inspecting and manipulating spectral libraries.""" - format_string = '[%(asctime)s] %(levelname).1s | %(name)s | %(message)s' - - logging.basicConfig( - level='INFO', - stream=sys.stderr, - format=format_string, - datefmt="%H:%M:%S") - - fmtr = ColoringFormatter(format_string, datefmt='%H:%M:%S') - - for handler in logging.getLogger().handlers: - handler.setFormatter( - fmtr - ) - - -@main.command("describe", short_help=("Produce a minimal textual description" - " of a spectral library")) -@click.argument('path', type=click.Path(exists=True)) -@click.option("-d", "--diagnostics", is_flag=True, - help="Run more diagnostics, greatly increasing runtime but producing additional information") -@click.option("-i", "--input-format", - type=click.Choice(sorted(SpectralLibraryBackendBase._file_extension_to_implementation)), - help='The file format of the input file. If omitted, will attempt to infer automatically.') -def describe(path, diagnostics=False, input_format=None): - """Produce a minimal textual description of a spectral library.""" - click.echo("Describing \"%s\"" % (path,)) - if SQLIndex.exists(path): - index_type = SQLIndex - else: - index_type = MemoryIndex - try: - library = SpectrumLibrary(filename=path, index_type=index_type, format=input_format) - except FormatInferenceFailure as err: - click.echo(f"{err}", err=True) - raise click.Abort() - click.echo(f"Format: {library.format}") - click.echo(f"Spectrum Count: {library.__len__()}") - for attr in library.attributes: - if not attr.group_id: - click.echo(f"{attr.key}={attr.value}") - else: - click.echo(f"[{attr.group_id}]{attr.key}={attr.value}") - - -@main.command("convert", short_help=("Convert a spectral library from one format to another")) -@click.argument('inpath', type=click.Path(exists=True)) -@click.argument("outpath", type=click.Path()) -@click.option("-i", "--input-format", type=click.Choice(sorted(SpectralLibraryBackendBase._file_extension_to_implementation))) -@click.option("-f", "--format", type=click.Choice(["text", "json", "msp"]), default="text") -@click.option("-k", "--library-attribute", "library_attributes", type=(str, str), multiple=True, - help="Specify an attribute to add to the library metadata section. May be repeated.") -@click.option("-K", "--header-file", type=click.Path(readable=True), - help="Specify a file to read name-value pairs from. May be JSON or TAB-separated") -def convert(inpath, outpath, format=None, header_file=None, library_attributes=(), input_format=None): - """ - Convert a spectral library from one format to another. If `outpath` is `-`, - instead of writing to file, data will instead be sent to STDOUT. - """ - if format is None: - format = "text" - if format == 'msp': - click.secho("MSP conversion is arbitrary and lossy", fg='yellow', err=True) - if SQLIndex.exists(inpath): - index_type = SQLIndex - else: - index_type = MemoryIndex - click.echo(f"Opening {inpath}", err=True) - try: - library = SpectrumLibrary(filename=inpath, index_type=index_type, format=input_format) - except FormatInferenceFailure as err: - click.echo(f"{err}", err=True) - raise click.Abort() - if header_file: - library_attributes = list(library_attributes) - if header_file.endswith(".json"): - library_attributes.extend( - json.load(open(header_file, 'rt')).items()) - else: - library_attributes.extend( - csv.reader(open(header_file, 'rt'), delimiter='\t')) - if library_attributes: - resolver = ControlledVocabularyResolver() - for k, v in library_attributes: - k = resolver.attribute_syntax(k) - library.add_attribute(k, v) - click.echo(f"Writing to {outpath}", err=True) - fh = click.open_file(outpath, mode='w') - try: - library.write(fh, format) - except IOError as err: - if outpath == '-': - return - else: - raise - - - _display_tree(library.summarize_parsing_errors()) - - -@main.command("index", short_help="Build an on-disk index for a spectral library") -@click.argument('inpath', type=click.Path(exists=True)) -@click.option("-i", "--input-format", type=click.Choice(sorted(SpectralLibraryBackendBase._file_extension_to_implementation))) -def build_index(inpath, input_format=None): - """Build an external on-disk SQL-based index for the spectral library""" - try: - library = SpectrumLibrary(filename=inpath, index_type=SQLIndex, format=input_format) - except FormatInferenceFailure as err: - click.echo(f"{err}", err=True) - raise click.Abort() - - -def _progress_logger(iterable, label, increment: int=100): - n = len(iterable) - for i, item in enumerate(iterable): - if i % increment == 0 and i: - logger.info(f"... {label} {i}/{n} ({i * 100 / n:0.2f}%)") - yield item - - -@main.command(short_help="Semantically validate a spectral library") -@click.argument('inpath', type=click.Path(exists=True)) -@click.option("-p", "--profile", "profiles", type=click.Choice( - ["consensus", "single", "silver", "peptide", "gold"], - case_sensitive=False), - multiple=True) -@click.option("-i", "--input-format", type=click.Choice(sorted(SpectralLibraryBackendBase._file_extension_to_implementation))) -def validate(inpath, profiles=None, input_format=None): - """Semantically and structurally validate a spectral library.""" - if profiles is None: - profiles = [] - if SQLIndex.exists(inpath): - index_type = SQLIndex - else: - index_type = MemoryIndex - - logger.info(f"Loading library {inpath}...") - try: - library = SpectrumLibrary(filename=inpath, index_type=index_type, format=input_format) - except FormatInferenceFailure as err: - click.echo(f"{err}", err=True) - raise click.Abort() - - logger.info(f"Loading validators...") - chain = validator.get_validator_for("base") - chain |= validator.get_object_validator_for("peak_annotations") - for profile in profiles: - if profile is None: - continue - logger.info(f"... {profile}") - chain |= validator.get_validator_for(profile) - - logger.info(f"Validating {inpath}...") - n_spectra = len(library) - increment = max(min(n_spectra // 10, 5000), 1) - chain.validate_library(library, _progress_logger(library, "Validating spectra", increment)) - - by_level: DefaultDict[RequirementLevel, List[validator.ValidationError]] = DefaultDict(list) - for message in chain.error_log: - by_level[message.requirement_level].append(message) - - for level, bucket in sorted(by_level.items()): - logger.info(f"Found {len(bucket)} violations for {level.name.upper()} rules") - for err in bucket: - logger.warn(f"... {err.message}") - - -if __name__ == "__main__": - main() diff --git a/implementations/python/mzlib/tools/utils.py b/implementations/python/mzlib/tools/utils.py deleted file mode 100644 index ff8d2d8..0000000 --- a/implementations/python/mzlib/tools/utils.py +++ /dev/null @@ -1,65 +0,0 @@ -import logging -import re -from typing import Dict - - -class LevelAwareColoredLogFormatter(logging.Formatter): - try: - from colorama import Fore, Style - # GREY = Fore.WHITE - GREY = '' - BLUE = Fore.BLUE - GREEN = Fore.GREEN - YELLOW = Fore.YELLOW - RED = Fore.RED - BRIGHT = Style.BRIGHT - DIM = Style.DIM - BOLD_RED = Fore.RED + Style.BRIGHT - RESET = Style.RESET_ALL - except ImportError: - GREY = '' - BLUE = '' - GREEN = '' - YELLOW = '' - RED = '' - BRIGHT = '' - DIM = '' - BOLD_RED = '' - RESET = '' - - def _colorize_field(self, fmt: str, field: str, color: str) -> str: - return re.sub("(" + field + ")", color + r"\1" + self.RESET, fmt) - - def _patch_fmt(self, fmt: str, level_color: str) -> str: - fmt = self._colorize_field(fmt, r"%\(asctime\)s", self.GREEN) - fmt = self._colorize_field(fmt, r"%\(name\).*?s", self.BLUE) - fmt = self._colorize_field(fmt, r"%\(message\).*?s", self.GREY) - if level_color: - fmt = self._colorize_field(fmt, r"%\(levelname\).*?s", level_color) - return fmt - - def __init__(self, fmt, level_color=None, **kwargs): - fmt = self._patch_fmt(fmt, level_color=level_color) - super().__init__(fmt, **kwargs) - - -class ColoringFormatter(logging.Formatter): - level_to_color = { - logging.INFO: LevelAwareColoredLogFormatter.GREEN, - logging.DEBUG: LevelAwareColoredLogFormatter.GREY + LevelAwareColoredLogFormatter.DIM, - logging.WARN: LevelAwareColoredLogFormatter.YELLOW + LevelAwareColoredLogFormatter.BRIGHT, - logging.ERROR: LevelAwareColoredLogFormatter.BOLD_RED, - logging.CRITICAL: LevelAwareColoredLogFormatter.BOLD_RED, - logging.FATAL: LevelAwareColoredLogFormatter.RED + LevelAwareColoredLogFormatter.DIM, - } - - _formatters: Dict[int, LevelAwareColoredLogFormatter] - - def __init__(self, fmt: str, **kwargs): - self._formatters = {} - for level, style in self.level_to_color.items(): - self._formatters[level] = LevelAwareColoredLogFormatter(fmt, level_color=style, **kwargs) - - def format(self, record: logging.LogRecord) -> str: - fmtr = self._formatters[record.levelno] - return fmtr.format(record) diff --git a/implementations/python/mzlib/universal_spectrum_identifier.py b/implementations/python/mzlib/universal_spectrum_identifier.py deleted file mode 100644 index bfddb44..0000000 --- a/implementations/python/mzlib/universal_spectrum_identifier.py +++ /dev/null @@ -1,281 +0,0 @@ -#!/usr/bin/env python3 -# pragma: no cover -from __future__ import print_function -import sys -def eprint(*args, **kwargs): - print(*args, file=sys.stderr, **kwargs) - -import re - -class UniversalSpectrumIdentifier(object): - - # usi object takes usiStr an automatically parses it and stores attributes - # usi objects can still exist even if the usi str is incorrect. - # it will simply show where the error in the string is - - def __init__(self, usi=None): - - self.is_valid = False - self.usi = usi - self.dataset_identifier = None - self.dataset_subfolder = None - self.ms_run_name = None - self.indexFlag = None - self.index = None - self.interpretation = None - self.peptidoform = None - self.charge = None - self.provenance_identifier = None - self.error = 0 - self.error_code = None - self.error_message = None - self.warning_message = None - - if usi: - self.parse(verbose=None) - - - # Attributes: - # usi - # dataset_identifier - # dataset_subfolder - # ms_run_name - # indexFlag - # index - # interpretation - # peptidoform - # charge - - - #### Set the error state with supplied information - def set_error(self,error_code,error_message): - self.error_code = error_code - self.error_message = error_message - self.is_valid = False - #print(f"ERROR: {error_code}: {error_message}") - - # parses USI string - def parse(self, verbose): - verboseprint = print if verbose else lambda *a, **k: None - verboseprint("\nINFO: Parsing USI string '" + self.usi + "'") - elementOffset = 0 - offset = 0 - if self.usi.startswith("mzspec:"): - self.usiMzspec = self.usi[len("mzspec:"):] - else: - self.set_error("MissingPrefix","USI does not begin with prefix 'mszpec:'") - return(self) - - # creates list of potential usi attributes - elements = self.usiMzspec.split(":") - nElements = len(elements) - # print(elements) - # print(nElements) - - # checks if usi has at least 4 colon-separated fields - if nElements < 4: - self.set_error("InsufficientComponents","USI string does not have the minimum required 4 colon-separated fields after mzspec:") - return(self) - - offset = elementOffset - - # dataset_identifier field - self.dataset_identifier = elements[offset] - if self.dataset_identifier is None: - self.set_error("EmptyDatasetIdentifier","Dataset identifier is empty. Not permitted.") - elif self.dataset_identifier.startswith("PXD") or self.dataset_identifier.startswith("PXL"): - self.dataset_identifier = elements[offset] - else: - self.set_error("UnrecognizedDatasetIdentifier","Dataset identifier unknown. Not permitted.") - self.error += 1 - - elementOffset += 1 - offset = elementOffset - nextField = elements[offset] - offsetShift = 0 - - #### The old style thing now clashes with the interest in leaving the version out of PXLs - # empty dataset_subfolder - #if nextField == '': - # self.warning_message = "old style. empty is ok. Empty dataset_subfolder probably." - # offsetShift = 1 - - offset = elementOffset + offsetShift - self.ms_run_name = elements[offset] - - if self.ms_run_name: - verboseprint("MS run equals " + self.ms_run_name) - else: - if self.dataset_identifier.startswith("PXL"): - verboseprint("For PXL identifiers, the version may be blank, okay.") - else: - self.set_error("MissingMSRunIdentifier","MS Run identifier empty. Not permitted.") - self.error += 1 - - elementOffset += 1 - offset = elementOffset + offsetShift - self.indexFlag = elements[offset] - # print("check " + self.indexFlag) - # does indexFlag exist? - if self.indexFlag: - # is it scan or index - if self.indexFlag == "scan" or self.indexFlag == "index": - verboseprint("indexFlag is OK.") - # is there potentially some weird colon escaping in the msRun name? - else: - potentialOffsetShift = offsetShift - appendStr = "" - repaired = False - - # fix colon escaping if it exists - while elementOffset + potentialOffsetShift < nElements: - # go until program finds 'scan' or 'index' index flag types - if elements[elementOffset + potentialOffsetShift].startswith("scan") or elements[ - elementOffset + potentialOffsetShift].startswith("index"): - self.indexFlag = elements[elementOffset + potentialOffsetShift] - self.ms_run_name += appendStr - offsetShift = potentialOffsetShift - repaired = True - break - appendStr += ":" + elements[elementOffset + potentialOffsetShift] - - potentialOffsetShift += 1 - - # colon escape fixed and msRun field updated - if repaired: - verboseprint("Unescaped colon in msRun name. Hopefully taken care of. Please fix this") - verboseprint("msRun name revised to '{}'".format(self.ms_run_name)) - - # no 'scan' or 'index' fields found later. assume broken index flag - else: - self.error += 1 - self.set_error("InvalidIndexType","Index type invalid. Must be 'scan' or 'index'") - - # no index flag - else: - self.error += 1 - self.set_error("MissingIndexType","Index flag empty! Not permitted.") - - elementOffset += 1 - offset = offsetShift + elementOffset - - # index for index flag if flag is valid. useless if index flag is invalid - self.index = elements[offset] - if self.index: - verboseprint("Index is " + self.index) - else: - self.set_error("MissingIndex","Index number empty! Not permitted.") - self.error += 1 - - elementOffset += 1 - offset = elementOffset + offsetShift - - # if statement check to see if the USI even has an interpretation field - if offset < nElements: - self.interpretation = elements[offset] - self.peptidoform = '' - self.charge = '' - if self.interpretation and self.interpretation != '': - find = re.match(r"^\s*(.+)\/(\d+)\s*$", self.interpretation) - # match - if find: - # subfields of interpretation - self.peptidoform = find.group(1) - self.charge = find.group(2) - verboseprint("Interpreted peptidoform = {}, charge = {}".format(self.peptidoform, self.charge)) - else: - self.set_error("MissingIndex","Unable to parse interpretation {} as peptidoform/charge".format(self.interpretation)) - - else: - verboseprint("Interpretation field not provided. OK.") - - # provenance identifier - if offset < nElements: - self.provenance_identifier = elements[offset] - verboseprint("Provenance Identifier = ".format(self.provenance_identifier)) - # returns count of errors found in usi. useful for checking if the entire identifier is valid. - - if self.error == 0: - self.is_valid = True - # errors found in usi - else: - verboseprint("Number of errors: " + str(self.error)) - self.is_valid = False - verboseprint("ERROR: Invalid USI " + self.usi) - - # prints out USI attributes - def show(self): - print("USI: " + str(self.usi)) - print("is_valid: " + str(self.is_valid)) - print("Dataset Identifier: " + str(self.dataset_identifier)) - print("Dataset Subfolder: " + str(self.dataset_subfolder)) - print("MS run name: " + str(self.ms_run_name)) - print("Index flag: " + str(self.indexFlag)) - print("Index: " + str(self.index)) - print("Peptidoform: " + str(self.peptidoform)) - print("Charge: " + str(self.charge)) - - -# If this class is run from the command line, perform a short little test to see if it is working correctly -def run_tests(): - testUSIs = [ - ["valid", "mzspec:PXD002437:00261_A06_P001564_B00E_A00_R1:scan:10951"], - ["invalid", "PXD002437:00261_A06_P001564_B00E_A00_R1:scan:10951"], - ["valid", "mzspec:PXD002437:00261_A06_P001564_B00E_A00_R1:scan:10951:PEPT[Phospho]IDELVISK/2"], - ["invalid", "mzspec:PASS002437:00261_A06_P001564_B00E_A00_R1:scan:10951:PEPT[Phospho]IDELVISK/2"], - ["invalid", "mzspec"], - ["invalid", "mzspec:"], - ["invalid", "mzspec:PXD001234"], - ["invalid", "mzspec:PXD001234:00261_A06_P001564_B00E_A00_R1:scan"], - ["valid", "mzspec:PXD001234:00261_A06_P001564_B00E_A00_R1:index:10951"], - ["valid", "mzspec:PXD002437:00261_A06_P001564_B00E_A00_R1:scan:10951:PEPT[Phospho]IDELVISK/2"], - ["valid", "mzspec:PXD002437:00261_A06_P001564_B00E_A00_R1:scan:10951:PEPT[+79]IDELVISK/2"], - ["valid", "mzspec:PXD001234:Dilution1:4:scan:10951"], - ["valid", "mzspec:PXD002437:00261_A06_P001564_B00E_A00_R1:test1:scan:10951:PEPT[Phospho]IDELVISK/2"], - ["valid", "mzspec:PXD002437:00261_A06_P001564_B00E_A00_R1\\:test1:scan:10951:PEPT[Phospho]IDELVISK/2"], - ] - testUSIsValid = [] - - # Loop over each test USI, parse it, and determine if it is valid or not, and print the index number - print("Testing example USIs:") - for usiSet in testUSIs: - expectedStatus = usiSet[0] - usiStr = usiSet[1] - - # Create a new UniversalSpectrumIdentifier object - # made the USI object itself take a string so that parse does not need to be called explicitly - usi = UniversalSpectrumIdentifier(usiStr) - expected_validity = True - if expectedStatus == 'invalid': - expected_validity = False - else: - expectedStatus = 'valid ' - - status = 'PASS' - if usi.is_valid is not expected_validity: - status = 'FAIL' - - response = usi.is_valid - testUSIsValid.append(response) - print(f"{status}\texpected {expectedStatus}\t{usiStr}") - # check to see if parsing is correct - #print(testUSIsValid) - - -#### A very simple example of using this class -def example(): - usiStr = "mzspec:PXD002437:00261_A06_P001564_B00E_A00_R1:scan:10951" - usiStr = "mzspec:PXL000001:01-09-2015:index:500" - usiStr = "mzspec:PXL000001::index:500" - usi = UniversalSpectrumIdentifier(usiStr) - #usi.parse(verbose=1) - usi.show() - - -#### If class is run directly -def main(): - #example() - run_tests() - - -if __name__ == "__main__": main() diff --git a/implementations/python/mzlib/utils.py b/implementations/python/mzlib/utils.py deleted file mode 100644 index 6f24904..0000000 --- a/implementations/python/mzlib/utils.py +++ /dev/null @@ -1,19 +0,0 @@ -from typing import Iterable, Any, Union, TypeVar - -T = TypeVar("T") - -def ensure_iter(obj: Union[Any, T, Iterable[T]]) -> Iterable[Union[Any, T]]: - if isinstance(obj, Iterable): - if not isinstance(obj, (str, bytes)): - return obj - return (obj, ) - - -def flatten(obj: Iterable[Union[Iterable[T], T]]) -> Iterable[T]: - acc = [] - for val in obj: - if isinstance(val, Iterable) and not isinstance(val, (str, bytes)): - acc.extend(flatten(val)) - else: - acc.append(val) - return acc diff --git a/implementations/python/mzlib/validate/__init__.py b/implementations/python/mzlib/validate/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/implementations/python/mzlib/validate/level.py b/implementations/python/mzlib/validate/level.py deleted file mode 100644 index 26d28c6..0000000 --- a/implementations/python/mzlib/validate/level.py +++ /dev/null @@ -1,35 +0,0 @@ -import enum - -class RequirementLevel(enum.IntEnum): - may = 0 - should = 1 - must = 2 - disallow = 3 - - @classmethod - def from_str(cls, text: str) -> 'RequirementLevel': - text = str(text).lower() - return cls[text] - - -class CombinationLogic(enum.Enum): - or_ = enum.auto() - and_ = enum.auto() - xor = enum.auto() - - @classmethod - def from_str(cls, text: str) -> 'CombinationLogic': - text = str(text).lower() - if text in ("or", "and"): - text += '_' - return cls[text] - - def to_str(self) -> str: - if self == self.or_: - return "OR" - elif self == self.and_: - return "AND" - elif self == self.xor: - return "XOR" - else: - raise ValueError(self) diff --git a/implementations/python/mzlib/validate/object_rule.py b/implementations/python/mzlib/validate/object_rule.py deleted file mode 100644 index 680352c..0000000 --- a/implementations/python/mzlib/validate/object_rule.py +++ /dev/null @@ -1,88 +0,0 @@ - -import logging - -from typing import TYPE_CHECKING, List, Tuple - -from mzlib.attributes import Attributed - -from mzlib.spectrum import Spectrum -from mzlib.annotation import IonAnnotationBase, InvalidAnnotation - -from mzlib.validate.level import RequirementLevel - -if TYPE_CHECKING: - from .validator import ValidatorBase - - -logger = logging.getLogger(__name__) -logger.addHandler(logging.NullHandler()) - - -class ValidationWarning(UserWarning): - """ - Indicates that something was parsed that did not halt the parser but - which violates the expectations of the parser. - - The parser will make a best-effort attempt to interpret the value - correctly but when validating this will count as a violation. - """ - - -class ScopedObjectRuleBase: - id: str - path: str - requirement_level: RequirementLevel - - def __init__(self, id, path: str, requirement_level: RequirementLevel=RequirementLevel.should) -> None: - self.id = id - self.path = path - self.requirement_level = requirement_level - - def __call__(self, obj: Attributed, path: str, identifier_path: Tuple, validator_context: "ValidatorBase") -> bool: - return self.validate(obj, path, identifier_path, validator_context) - - def validate(self, obj: Attributed, path: str, identifier_path: Tuple, validator_context: "ValidatorBase") -> bool: - raise NotImplementedError() - - -class SpectrumPeakAnnotationRule(ScopedObjectRuleBase): - def __init__(self, requirement_level: RequirementLevel=RequirementLevel.should): - super().__init__( - "Spectrum_peak_annotation_rule", "/Library/Spectrum", requirement_level=requirement_level) - - def validate(self, obj: Spectrum, path: str, identifier_path: Tuple, validator_context: "ValidatorBase") -> bool: - errors = [] - for i, peak in enumerate(obj.peak_list): - annotations = peak[2] - annotations: List[IonAnnotationBase] - for annot in annotations: - if isinstance(annot, InvalidAnnotation): - errors.append(annot) - validator_context.add_warning( - obj, - path, - identifier_path, - self, - annot, - self.requirement_level, - f"Invalid peak annotation for peak {i} of Spectrum={obj.key} {annot.content}" - ) - else: - analyte_id = annot.analyte_reference - if analyte_id is not None: - if analyte_id not in obj.analytes: - validator_context.add_warning( - obj, - path, - identifier_path, - self, - annot, - self.requirement_level, - (f"Analyte of peak annotation {annot} for peak {i} of " - f"Spectrum={obj.key} {annot.analyte_reference} is missing") - ) - - - if errors: - return False - return True diff --git a/implementations/python/mzlib/validate/rules/__init__.py b/implementations/python/mzlib/validate/rules/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/implementations/python/mzlib/validate/rules/all.json b/implementations/python/mzlib/validate/rules/all.json deleted file mode 100644 index de143c4..0000000 --- a/implementations/python/mzlib/validate/rules/all.json +++ /dev/null @@ -1,1578 +0,0 @@ -{ - "$schema": "./validator-rules-schema.json", - "name": "all_metadata", - "rules": [ - { - "id": "has_library_format_version", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003186", - "name": "library format version", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MUST" - }, - { - "id": "has_library_identifier", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003187", - "name": "library identifier", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "SHOULD" - }, - { - "id": "has_library_name", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003188", - "name": "library name", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MUST" - }, - { - "id": "has_library_description", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003189", - "name": "library description", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_library_version", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003190", - "name": "library version", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_library_uri", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003191", - "name": "library URI", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_release_date", - "path": "/Library", - "attr": [ - { - "accession": "MS:1001017", - "name": "release date", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:datetime" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_reference", - "path": "/Library", - "attr": [ - { - "accession": "MS:1002866", - "name": "Reference", - "repeatable": true, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_digital_object_identifier_(doi)", - "path": "/Library", - "attr": [ - { - "accession": "MS:1001922", - "name": "Digital Object Identifier (DOI)", - "repeatable": true, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_pubmed_identifier", - "path": "/Library", - "attr": [ - { - "accession": "MS:1000879", - "name": "PubMed identifier", - "repeatable": true, - "value": { - "name": "value_of_type", - "value": "xsd:integer" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_license_uri", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003197", - "name": "license URI", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_copyright_notice", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003198", - "name": "copyright notice", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_change_log", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003199", - "name": "change log", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_contact_name", - "path": "/Library", - "attr": [ - { - "accession": "MS:1000586", - "name": "contact name", - "repeatable": true, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_contact_address", - "path": "/Library", - "attr": [ - { - "accession": "MS:1000587", - "name": "contact address", - "repeatable": true, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_contact_url", - "path": "/Library", - "attr": [ - { - "accession": "MS:1000588", - "name": "contact URL", - "repeatable": true, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_contact_affiliation", - "path": "/Library", - "attr": [ - { - "accession": "MS:1000590", - "name": "contact affiliation", - "repeatable": true, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_contact_email", - "path": "/Library", - "attr": [ - { - "accession": "MS:1000589", - "name": "contact email", - "repeatable": true, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_contact_role", - "path": "/Library", - "attr": [ - { - "accession": "MS:1002033", - "name": "contact role", - "repeatable": true, - "value": { - "name": "value_is_child_of", - "accession": "MS:1002033" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_library_creation_software", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003207", - "name": "library creation software", - "repeatable": false, - "value": { - "name": "value_is_child_of", - "accession": "MS:1003207" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_software_version", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003200", - "name": "software version", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_library_creation_log", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003206", - "name": "library creation log", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_command-line_parameters", - "path": "/Library", - "attr": [ - { - "accession": "MS:1001885", - "name": "command-line parameters", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_constituent_spectrum_file", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003203", - "name": "constituent spectrum file", - "repeatable": true, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_constituent_identification_file", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003205", - "name": "constituent identification file", - "repeatable": true, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_constituent_library_file", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003205", - "name": "constituent library file", - "repeatable": true, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_library_attribute_set_name", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003212", - "name": "library attribute set name", - "repeatable": true, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_spectrum_cluster_key", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003267", - "name": "spectrum cluster key", - "repeatable": true, - "value": { - "name": "value_of_type", - "value": "xsd:integer" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_spectrum_cluster_member_spectrum_keys", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003268", - "name": "spectrum cluster member spectrum keys", - "repeatable": true - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_spectrum_cluster_member_usi", - "path": "/Library", - "attr": [ - { - "accession": "MS:1003269", - "name": "spectrum cluster member USI", - "repeatable": true, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_library_spectrum_key", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003237", - "name": "library spectrum key", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:integer" - } - } - ], - "requirement_level": "MUST" - }, - { - "id": "has_library_spectrum_index", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003062", - "name": "library spectrum index", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:integer" - } - } - ], - "requirement_level": "MUST" - }, - { - "id": "has_library_spectrum_name", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003061", - "name": "library spectrum name", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_universal_spectrum_identifier", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003063", - "name": "universal spectrum identifier", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_splash_key", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1002599", - "name": "splash key", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_library_spectrum_comment", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003168", - "name": "library spectrum comment", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_ms_level", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000511", - "name": "ms level", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:integer" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_ionization_type", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000008", - "name": "ionization type", - "repeatable": false, - "value": { - "name": "value_is_child_of", - "accession": "MS:1000008" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_instrument_model", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000031", - "name": "instrument model", - "repeatable": false, - "value": { - "name": "value_is_child_of", - "accession": "MS:1000031" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_mass_analyzer_type", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000443", - "name": "mass analyzer type", - "repeatable": false, - "value": { - "name": "value_is_child_of", - "accession": "MS:1000443" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_dissociation_method", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000044", - "name": "dissociation method", - "repeatable": false, - "value": { - "name": "value_is_child_of", - "accession": "MS:1000044" - } - } - ], - "requirement_level": "SHOULD" - }, - { - "id": "has_mass_spectrometry_acquisition_method", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003213", - "name": "mass spectrometry acquisition method", - "repeatable": true, - "value": { - "name": "value_is_child_of", - "accession": "MS:1003213" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_collision_gas", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000419", - "name": "collision gas", - "repeatable": true, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_collision_energy", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000045", - "name": "collision energy", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "SHOULD" - }, - { - "id": "has_normalized_collision_energy", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000138", - "name": "normalized collision energy", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_experimental_precursor_monoisotopic_m/z", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003208", - "name": "experimental precursor monoisotopic m/z", - "repeatable": false, - "notes": "NOTE: This is the preferred term for specification of the precursor m/z in typical use cases. If the specification of the isolation window is desired, the terms MS:1000827|isolation window target m/z, MS:1000828|isolation window lower offset, MS:1000829|isolation window upper offset should be used. The terms MS:1000744|selection ion m/z and MS:1002234|selection precursor m/z are unclear and should be avoided.", - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MUST" - }, - { - "id": "has_isolation_window_target_m/z", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000827", - "name": "isolation window target m/z", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_isolation_window_lower_offset", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000828", - "name": "Isolation window lower offset", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_isolation_window_upper_offset", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000829", - "name": "Isolation window upper offset", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_retention_time", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000894", - "name": "retention time", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_normalized_retention_time", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000896", - "name": "normalized retention time", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_retention_time_normalization_standard", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000901", - "name": "retention time normalization standard", - "repeatable": false, - "value": { - "name": "value_is_child_of", - "accession": "MS:1000901" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_ion_mobility_drift_time", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1002476", - "name": "ion mobility drift time", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_inverse_reduced_ion_mobility", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1002875", - "name": "inverse reduced ion mobility", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_collision_cross_sectional_area", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1002954", - "name": "collision cross sectional area", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:double" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_faims_compensation_voltage", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1001581", - "name": "FAIMS compensation voltage", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:double" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_scan_polarity", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000465", - "name": "scan polarity", - "repeatable": false, - "value": { - "name": "value_is_child_of", - "accession": "MS:1000465" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_filter_string", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000512", - "name": "filter string", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_mass_resolution", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000011", - "name": "mass resolution", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_mass_resolving_power", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000800", - "name": "mass resolving power", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_precursor_apex_intensity", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003086", - "name": "precursor apex intensity", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_previous_msn-1_scan_precursor_intensity", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003085", - "name": "previous MSn-1 scan precursor intensity", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:double" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_possible_charge_state", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000633", - "name": "possible charge state", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:integer" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_charge_state", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000041", - "name": "charge state", - "repeatable": false, - "notes": "The 'charge state' attribute has two different meanings depending on its context. When this attribute is included under , it is used to denote the experimental charge state of the precursor as inferred from the data (e.g. by the isotopic pattern of the precursor peak in the MSn-1 spectrum). If the spectrum is identified to an analyte, the charge state refers to that of the analyte believed to produce this spectrum. In such cases, the charge state attribute should be included in the section instead.", - "value": { - "name": "value_of_type", - "value": "xsd:integer" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_number_of_peaks", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003059", - "name": "number of peaks", - "repeatable": false, - "notes": "This is the preferred term for a peak-picked (centroid) spectrum. Use the term 'MS:1003060|number of data point' for a non-peak-picked (profile) spectrum.", - "value": { - "name": "value_of_type", - "value": "xsd:integer" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_number_of_data_points", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003060", - "name": "number of data points", - "repeatable": false, - "notes": "This is the preferred term for a non-peak-picked (profile) spectrum. Use the term 'MS:1003059|number of peaks' for a peak-picked (centroid) spectrum.", - "value": { - "name": "value_of_type", - "value": "xsd:integer" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_intensity_unit", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000034", - "name": "intensity unit", - "repeatable": false, - "value": { - "name": "value_is_child_of", - "accession": "MS:1000034" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_base_peak_intensity", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000505", - "name": "base peak intensity", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_signal-to-noise_ratio", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1001884", - "name": "signal-to-noise ratio", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_total_ion_current", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000285", - "name": "total ion current", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_spectrum_representation", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000525", - "name": "spectrum representation", - "repeatable": false, - "value": { - "name": "value_is_child_of", - "accession": "MS:1000525" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_data_processing_action", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1000543", - "name": "data processing action", - "repeatable": true, - "value": { - "name": "value_is_child_of", - "accession": "MS:1000543" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_spectrum_origin_type", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003072", - "name": "spectrum origin type", - "repeatable": false, - "value": { - "name": "value_is_child_of", - "accession": "MS:1003072" - } - } - ], - "requirement_level": "SHOULD" - }, - { - "id": "has_spectrum_aggregation_type", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003065", - "name": "spectrum aggregation type", - "repeatable": false, - "value": { - "name": "value_is_child_of", - "accession": "MS:1003065" - } - } - ], - "requirement_level": "SHOULD" - }, - { - "id": "has_ion_annotation_format", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003103", - "name": "ion annotation format", - "repeatable": false, - "value": { - "name": "value_is_child_of", - "accession": "MS:1003103" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_number_of_replicate_spectra_used", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003070", - "name": "number of replicate spectra used", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:integer" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_number_of_replicate_spectra_available", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003069", - "name": "number of replicate spectra available", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:integer" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_summary_statistics_of_replicate_spectra", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003295", - "name": "summary statistics of replicate spectra", - "repeatable": true, - "notes": "It should appear in a group with MS:1003174 - MS:1003180 to specify the type and value of the summary statistic.", - "value": { - "name": "value_is_child_of", - "accession": "MS:1003295" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_number_of_replicate_spectra_from_source", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003296", - "name": "number of replicate spectra from source", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_contributing_replicate_spectrum_keys", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003298", - "name": "contributing replicate spectrum keys", - "repeatable": false - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_contributing_replicate_spectrum_usi", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003299", - "name": "contributing replicate spectrum USI", - "repeatable": false - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_related_spectrum_keys", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003259", - "name": "related spectrum keys", - "repeatable": false - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_related_spectrum_usi", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003260", - "name": "related spectrum USI", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_related_spectrum_description", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003261", - "name": "related spectrum description", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_similar_spectrum_keys", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003263", - "name": "similar spectrum keys", - "repeatable": false - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_similar_spectrum_usi", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003264", - "name": "similar spectrum USI", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_peak_attribute", - "path": "/Library/Spectrum", - "attr": [ - { - "accession": "MS:1003254", - "name": "peak attribute", - "repeatable": true, - "value": { - "name": "value_is_child_of", - "accession": "MS:1003254" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_charge_state", - "path": "/Library/Spectrum/Analyte", - "attr": [ - { - "accession": "MS:1000041", - "name": "charge state", - "repeatable": false, - "notes": "The 'charge state' attribute has two different meanings depending on its context. When this attribute is included under , it is used to denote the experimental charge state of the precursor as inferred from the data (e.g. by the isotopic pattern of the precursor peak in the MSn-1 spectrum). If the spectrum is identified to an analyte, the charge state refers to that of the analyte believed to produce this spectrum. In such cases, the charge state attribute should be included in the section instead.", - "value": { - "name": "value_of_type", - "value": "xsd:integer" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_theoretical_mass", - "path": "/Library/Spectrum/Analyte", - "attr": [ - { - "accession": "MS:1001117", - "name": "theoretical mass", - "repeatable": false, - "notes": "This is the theoretical mass of the neutral molecule (does not include the charge-giving moiety. Use the term 'MS:1003243|adduct ion mass' to refer to the mass of the adduct ion, which includes the charge-giving moiety.", - "value": { - "name": "value_of_type", - "value": "xsd:double" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_adduct_ion_mass", - "path": "/Library/Spectrum/Analyte", - "attr": [ - { - "accession": "MS:1003243", - "name": "adduct ion mass", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_adduct_ion_formula", - "path": "/Library/Spectrum/Analyte", - "attr": [ - { - "accession": "MS:1002813", - "name": "adduct ion formula", - "repeatable": false, - "notes": "For peptides, absence of this field implies that the adduct ion is [M+nH]n+ where n is the charge state. The regular expression for this field is given in the definition of MS:1002812|Regular expression for adduct ion formula.", - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_theoretical_monoisotopic_m/z", - "path": "/Library/Spectrum/Analyte", - "attr": [ - { - "accession": "MS:1003053", - "name": "theoretical monoisotopic m/z", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_theoretical_average_m/z", - "path": "/Library/Spectrum/Analyte", - "attr": [ - { - "accession": "MS:1003054", - "name": "theoretical average m/z", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:float" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_taxonomy:_scientific_name", - "path": "/Library/Spectrum/Analyte", - "attr": [ - { - "accession": "MS:1001469", - "name": "taxonomy: scientific name", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_taxonomy:_common_name", - "path": "/Library/Spectrum/Analyte", - "attr": [ - { - "accession": "MS:1001468", - "name": "taxonomy: common name", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_taxonomy:_ncbi_taxid", - "path": "/Library/Spectrum/Analyte", - "attr": [ - { - "accession": "MS:1001467", - "name": "taxonomy: NCBI TaxID", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_sample_label", - "path": "/Library/Spectrum/Analyte", - "attr": [ - { - "accession": "MS:1002602", - "name": "sample label", - "repeatable": false, - "value": { - "name": "value_is_child_of", - "accession": "MS:1002602" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_sample_name", - "path": "/Library/Spectrum/Analyte", - "attr": [ - { - "accession": "MS:1000002", - "name": "sample name", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - }, - { - "id": "has_smiles_formula", - "path": "/Library/Spectrum/Analyte", - "attr": [ - { - "accession": "MS:1000868", - "name": "SMILES formula", - "repeatable": false, - "value": { - "name": "value_of_type", - "value": "xsd:string" - } - } - ], - "requirement_level": "MAY" - } - ] -} diff --git a/implementations/python/mzlib/validate/rules/base.json b/implementations/python/mzlib/validate/rules/base.json deleted file mode 100644 index d22733c..0000000 --- a/implementations/python/mzlib/validate/rules/base.json +++ /dev/null @@ -1,173 +0,0 @@ -{ - "$schema": "./validator-rules-schema.json", - "name": "base", - "rules": [ - { - "attr": [ - { - "accession": "MS:1003186", - "allow_children": false, - "name": "library format version", - "repeatable": false - } - ], - "combination_logic": "OR", - "id": "Library_has_format_version", - "level": "MUST", - "path": "/Library" - }, - { - "attr": [ - { - "accession": "MS:1003188", - "allow_children": false, - "name": "library name", - "repeatable": false - } - ], - "combination_logic": "OR", - "id": "Library_has_name", - "level": "MUST", - "path": "/Library" - }, - { - "attr": [ - { - "accession": "MS:1003237", - "allow_children": false, - "name": "library spectrum key", - "repeatable": false, - "value": "value_is_unique" - } - ], - "combination_logic": "OR", - "id": "Spectrum_has_unique_key", - "level": "MUST", - "path": "/Library/Spectrum" - }, - { - "attr": [ - { - "accession": "MS:1003062", - "allow_children": false, - "name": "library spectrum index", - "repeatable": false, - "value": "value_is_unique" - } - ], - "combination_logic": "OR", - "id": "Spectrum_has_index", - "level": "MUST", - "path": "/Library/Spectrum" - }, - { - "attr": [ - { - "accession": "MS:1003062", - "allow_children": false, - "name": "library spectrum index", - "repeatable": false, - "value": "value_is_unique" - } - ], - "combination_logic": "OR", - "id": "Spectrum_has_index", - "level": "MUST", - "path": "/Library/Spectrum" - }, - { - "attr": [ - { - "accession": "MS:1000041", - "allow_children": false, - "name": "charge state", - "repeatable": false - }, - { - "accession": "MS:1000633", - "allow_children": false, - "name": "possible charge state", - "repeatable": false - } - ], - "combination_logic": "OR", - "id": "Spectrum_has_precursor_charge", - "level": "MAY", - "path": "/Library/Spectrum" - }, - { - "attr": [ - { - "accession": "MS:1000744", - "allow_children": false, - "name": "selected ion m/z", - "repeatable": false - }, - { - "accession": "MS:1003208", - "allow_children": false, - "name": "experimental precursor monoisotopic m/z", - "repeatable": false - } - ], - "combination_logic": "OR", - "id": "Spectrum_has_precursor_mz", - "level": "SHOULD", - "path": "/Library/Spectrum" - }, - { - "attr": [ - { - "accession": "MS:1003065", - "allow_children": true, - "name": "spectrum aggregation type", - "repeatable": false - } - ], - "combination_logic": "OR", - "id": "Spectrum_has_aggregation", - "level": "SHOULD", - "path": "/Library/Spectrum" - }, - { - "attr": [ - { - "accession": "MS:1001117", - "allow_children": true, - "name": "theoretical mass", - "repeatable": false - }, - { - "accession": "MS:1000224", - "allow_children": true, - "name": "molecular mass", - "repeatable": false - } - ], - "combination_logic": "OR", - "id": "Analyte_has_any_mass", - "level": "SHOULD", - "path": "/Library/Spectrum/Analyte" - }, - { - "attr": [ - { - "accession": "MS:1000041", - "allow_children": false, - "name": "charge state", - "repeatable": false - }, - { - "accession": "MS:1000633", - "allow_children": false, - "name": "possible charge state", - "repeatable": false - } - ], - "combination_logic": "OR", - "id": "Analyte_has_charge", - "level": "SHOULD", - "path": "/Library/Spectrum/Analyte" - } - ] -} \ No newline at end of file diff --git a/implementations/python/mzlib/validate/rules/consensus.json b/implementations/python/mzlib/validate/rules/consensus.json deleted file mode 100644 index 17bd060..0000000 --- a/implementations/python/mzlib/validate/rules/consensus.json +++ /dev/null @@ -1,36 +0,0 @@ -{ - "$schema": "./validator-rules-schema.json", - "name": "consensus", - "rules": [ - { - "attr": [ - { - "accession": "MS:1003069", - "allow_children": false, - "name": "number of replicate spectra available", - "repeatable": false - }, - { - "accession": "MS:1003070", - "allow_children": false, - "name": "number of replicate spectra used", - "repeatable": false - } - ], - "combination_logic": "AND", - "id": "Spectrum_has_replicates_used", - "level": "SHOULD", - "path": "/Library/Spectrum", - "condition": { - "accession": "MS:1003072", - "allow_children": true, - "name": "spectrum origin type", - "repeatable": false, - "value": { - "name": "value_matches", - "accession": "MS:1003067" - } - } - } - ] -} \ No newline at end of file diff --git a/implementations/python/mzlib/validate/rules/gold.json b/implementations/python/mzlib/validate/rules/gold.json deleted file mode 100644 index 9c62549..0000000 --- a/implementations/python/mzlib/validate/rules/gold.json +++ /dev/null @@ -1,58 +0,0 @@ -{ - "$schema": "./validator-rules-schema.json", - "name": "gold", - "rules": [ - { - "attr": [ - { - "accession": "MS:1000586", - "allow_children": false, - "name": "contact name", - "repeatable": false - }, - { - "accession": "MS:1000587", - "allow_children": false, - "name": "contact address", - "repeatable": false - }, - { - "accession": "MS:1000588", - "allow_children": false, - "name": "contact URL", - "repeatable": false - }, - { - "accession": "MS:1000589", - "allow_children": false, - "name": "contact email", - "repeatable": false - }, - { - "accession": "MS:1000590", - "allow_children": false, - "name": "contact affilation", - "repeatable": false - } - ], - "combination_logic": "OR", - "id": "Library_has_contact", - "level": "SHOULD", - "path": "/Library" - }, - { - "attr": [ - { - "accession": "MS:1002866", - "allow_children": false, - "name": "Reference", - "repeatable": false - } - ], - "combination_logic": "OR", - "id": "Library_has_reference", - "level": "SHOULD", - "path": "/Library" - } - ] -} \ No newline at end of file diff --git a/implementations/python/mzlib/validate/rules/peptide.json b/implementations/python/mzlib/validate/rules/peptide.json deleted file mode 100644 index 08d8dc7..0000000 --- a/implementations/python/mzlib/validate/rules/peptide.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "$schema": "./validator-rules-schema.json", - "name": "peptide", - "rules": [ - { - "attr": [ - { - "accession": "MS:1000889", - "allow_children": false, - "name": "proforma peptidoform sequence", - "repeatable": false - }, - { - "accession": "MS:1000888", - "allow_children": false, - "name": "stripped peptide sequence", - "repeatable": false - }, - { - "accession": "MS:1003270", - "allow_children": false, - "name": "proforma peptidoform ion notation", - "repeatable": false - } - ], - "combination_logic": "OR", - "id": "Analyte_has_peptide_seq", - "level": "MUST", - "path": "/Library/Spectrum/Analyte" - } - ] -} \ No newline at end of file diff --git a/implementations/python/mzlib/validate/rules/silver.json b/implementations/python/mzlib/validate/rules/silver.json deleted file mode 100644 index 85ebb8a..0000000 --- a/implementations/python/mzlib/validate/rules/silver.json +++ /dev/null @@ -1,48 +0,0 @@ -{ - "$schema": "./validator-rules-schema.json", - "name": "silver", - "rules": [ - { - "attr": [ - { - "accession": "MS:1003187", - "allow_children": false, - "name": "library identifier", - "repeatable": false - } - ], - "combination_logic": "OR", - "id": "Library_has_identifier", - "level": "SHOULD", - "path": "/Library" - }, - { - "attr": [ - { - "accession": "MS:1003072", - "allow_children": true, - "name": "spectrum origin type", - "repeatable": false - } - ], - "combination_logic": "OR", - "id": "Spectrum_has_origin_type", - "level": "SHOULD", - "path": "/Library/Spectrum" - }, - { - "attr": [ - { - "accession": "MS:1000044", - "allow_children": true, - "name": "dissociation method", - "repeatable": false - } - ], - "combination_logic": "OR", - "id": "Spectrum_has_dissociation", - "level": "SHOULD", - "path": "/Library/Spectrum" - } - ] -} \ No newline at end of file diff --git a/implementations/python/mzlib/validate/rules/single.json b/implementations/python/mzlib/validate/rules/single.json deleted file mode 100644 index 21872e1..0000000 --- a/implementations/python/mzlib/validate/rules/single.json +++ /dev/null @@ -1,54 +0,0 @@ -{ - "$schema": "./validator-rules-schema.json", - "name": "single", - "rules": [ - { - "attr": [ - { - "accession": "MS:1000577", - "allow_children": false, - "name": "source file", - "repeatable": false - } - ], - "combination_logic": "OR", - "id": "Spectrum_has_source_file", - "level": "SHOULD", - "path": "/Library/Spectrum", - "condition": { - "accession": "MS:1003072", - "allow_children": true, - "name": "spectrum origin type", - "repeatable": false, - "value": { - "name": "value_matches", - "accession": "MS:1003066" - } - } - }, - { - "attr": [ - { - "accession": "MS:1003057", - "allow_children": false, - "name": "scan number", - "repeatable": false - } - ], - "combination_logic": "OR", - "id": "Spectrum_has_scan_identifier", - "level": "SHOULD", - "path": "/Library/Spectrum", - "condition": { - "accession": "MS:1003072", - "allow_children": true, - "name": "spectrum origin type", - "repeatable": false, - "value": { - "name": "value_matches", - "accession": "MS:1003066" - } - } - } - ] -} \ No newline at end of file diff --git a/implementations/python/mzlib/validate/rules/tmp/README.md b/implementations/python/mzlib/validate/rules/tmp/README.md deleted file mode 100644 index 668e27b..0000000 --- a/implementations/python/mzlib/validate/rules/tmp/README.md +++ /dev/null @@ -1,10 +0,0 @@ -# Temporary sheet with metadata terms - -Excel sheet of metadata terms as discussed during mzSpecLib development. This sheet is temporary -and will be replaced a JSON file that can be used for mzSpecLib validation and automatic generation -of documentation in markdown. - -Run the script `excel_terms_to_json_rules.py` to generate the JSON file. Then a Python script will -be run in GitHub Actions to convert this JSON file to markdown documentation. - -This folder and its contents can be removed in the future. diff --git a/implementations/python/mzlib/validate/rules/tmp/excel_terms_to_json_rules.py b/implementations/python/mzlib/validate/rules/tmp/excel_terms_to_json_rules.py deleted file mode 100644 index 732b3d9..0000000 --- a/implementations/python/mzlib/validate/rules/tmp/excel_terms_to_json_rules.py +++ /dev/null @@ -1,71 +0,0 @@ -import json -from pathlib import Path - -import pandas as pd -from jsonschema import validate - - -def excel_terms_to_dict(excel_file, sheet_name): - terms_sheet = pd.read_excel(excel_file, sheet_name=sheet_name) - # Remove trailing spaces from all dataframe values - terms_sheet = terms_sheet.apply( - lambda x: x.str.strip() if x.dtype == "object" else x - ) - terms = terms_sheet.to_dict(orient="records") - return terms - - -def parse_terms(terms): - """Translate terms from excel to metadata rules.""" - for term in terms: - attribute = { - "accession": term["accession"], - "name": term["name"], - "repeatable": term["repeatable"], - } - - if isinstance(term["notes"], str): - attribute["notes"] = term["notes"] - - if term["value"].startswith("Children of"): - attribute["value"] = { - "name": "value_is_child_of", - "accession": term["value"].split("Children of ")[1].strip(), - } - elif term["value"].startswith("xsd:"): - attribute["value"] = {"name": "value_of_type", "value": term["value"]} - yield { - "id": "has_" + term["name"].lower().replace(" ", "_"), - "path": term["path"], - "attr": [attribute], - "requirement_level": term["level"], - } - - -def main(schema_file, excel_file, sheet_name, json_file): - # Read Excel - terms = excel_terms_to_dict(excel_file, sheet_name) - - # Parse terms to validation rules - rules = { - "$schema": "./validator-rules-schema.json", - "name": "all_metadata", - "rules": [t for t in parse_terms(terms)], - } - - # Validate - validate(rules, json.load(open(schema_file))) - - # Write JSON - with open(json_file, "w") as f: - json.dump(rules, f, indent=2) - - -if __name__ == "__main__": - current_path = Path(__file__).parent - schema_file = current_path / "../validator-rules-schema.json" - excel_file = current_path / "terms.xlsx" - sheet_name = "general" - json_file = current_path / "../all.json" - - main(schema_file, excel_file, sheet_name, json_file) diff --git a/implementations/python/mzlib/validate/rules/tmp/terms.xlsx b/implementations/python/mzlib/validate/rules/tmp/terms.xlsx deleted file mode 100644 index 055a6ac7c8fc9c462ad26a19e53a096793190d69..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 25472 zcmeFYQ~;>tS*?5a`s!63dCX) z7t8HY8S8+M1HLY$Z94CKAyqW~3W*=&6b^OrKS5{G_S)k zx+M3?M_@wFUU%{39ifoaNNQ_SrJ+;BA3wGQQzDJOj~|4qmTIbgMid@~_aEeH{jR~_ z6vpE-qXsOkmdAr;3PymhV?eg2Gx3F*CfaP3Xk&yLm~-tkI0r{h&l;#^b;9G0)@3FZ zL^;t~ywIYhdOhs7+}oh$fwi}`(2tl?$LLt}3gpEV!O+Q~`epVZyu;+=_#GDg&O68N zdCWI_d`J{VPX^}OSPoG0i6t_l@V5vmS9Gw&&D{x*w=U*%ClmwhI8K4O_f=~}L_}fp z4jRM{`a-~9`*5AX9z=V?*_2T^U~7QJp!m7xhnL^qzyN>#AB=5Mq9=OzQA4R8LjL+; ztd6~rr2`%9Kkffv>i@>{{BKjQjF*-jpob2=7W)VpeO}y*g%^-?;TP*5Q1tc{-+*h1 zDj>$%>>NUC3xCnu8crL<|1l#sR~YcvvUHcB(+Z#v8&u2 zL~vewTzpCsm2e|>?uwzTXf4f?9NQ)mnZFgPgP*2V!GuIA!VX5|N%K=5mR8%+f2jss z6i~RV3a)Ko%RNh&&hS}IE27`++ukH9P4`X5O` zwW}D}0So}30to;B_p>stmUJ#Q_7?g!HWvT5v`Qr_n*w(DFYmce@Ie=-BN|9btspk7 zB4?$dRcG07#Wr1krQS>iY4^piXDmUnd1I$>Cpw9X6cS@n@i7CN8JQjKNhjX=v7v})3xk3o%RDG}Q~T-)?t52GsyKmbnX6+!S(CFfS^ zu~020l>{uA2azhOz40}V&AT8bR{Wu*5}VA>DmC;~i-3LmCAziTB@|(*Yf6Qvzz}34 zsC+#%rt{IJO72jaL9YtSrW6&JzOIEND0Dof<%(r4ZPgefF(j>B!qN4IH%_}D(CB|} zN!dBu%kwErXeNd*_|Ab(iN53Vh#qJ`*7wmfgALC!xfRj|c&M(t^GA1Aq8-E^B6TB$^NK)Y?`@T? 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file mode 100644 index edbdafa..0000000 --- a/implementations/python/mzlib/validate/rules/validator-rules-schema.json +++ /dev/null @@ -1,216 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft-07/schema#", - "title": "Semantic Validtion Rule Format", - "description": "Specify how to semantically validate a format", - "type": "object", - "additionalProperties": true, - "required": [ - "rules" - ], - "properties": { - "rules": { - "type": "array", - "items": { - "type": "object", - "$ref": "#/definitions/scoped_semantic_rule" - } - }, - "name": { - "type": "string", - "description": "The name for the specific set of validation rules" - } - }, - "definitions": { - "attribute_semantic_predicate": { - "description": "A rule for evaluating an attribute-value pair", - "required": [ - "name" - ], - "additionalProperties": true, - "properties": { - "name": { - "type": "string", - "description": "The name of the rule", - "enum": [ - "value_matches", - "value_is_unique", - "value_is_child_of", - "value_of_type", - "value_matches_pattern" - ] - } - } - }, - "value_is_child_of_predicate": { - "type": "object", - "allOf": [ - { - "$ref": "#/definitions/attribute_semantic_predicate" - } - ], - "properties": { - "accession": { - "type": "string", - "description": "The accession of the term that children of are valid" - } - } - }, - "value_of_type": { - "type": "object", - "allOf": [ - { - "$ref": "#/definitions/attribute_semantic_predicate" - } - ], - "properties": { - "type_name": { - "type": "string", - "description": "The name of the expected type" - } - } - }, - "value_is_unique": { - "type": "object", - "allOf": [ - { - "$ref": "#/definitions/attribute_semantic_predicate" - } - ], - "additionalProperties": false - }, - "value_matches": { - "type": "object", - "allOf": [ - { - "$ref": "#/definitions/attribute_semantic_predicate" - } - ], - "properties": { - "accession": { - "type": "string", - "description": "The accession of the term that must be matched exactly" - } - } - }, - "value_matches_pattern": { - "type": "object", - "allOf": [ - { - "$ref": "#/definitions/attribute_semantic_predicate" - } - ], - "properties": { - "pattern": { - "type": "string", - "description": "The value of the term that must match this ECMAScript Regular Expression, interpreted as a string" - } - } - }, - "semantic_attribute_rule": { - "description": "An attribute to match", - "required": [ - "accession" - ], - "properties": { - "accession": { - "type": "string", - "description": "The accession number for the controlled vocabulary term being used" - }, - "name": { - "type": "string", - "description": "The name of the controlled vocabulary term being used", - "default": null - }, - "allow_children": { - "type": "boolean", - "description": "Whether or not this rule is allowed to match children of the named term", - "default": false - }, - "repeatable": { - "type": "boolean", - "description": "Whether the rule may match the same attribute multiple times", - "default": false - }, - "value": { - "anyOf": [ - { - "$ref": "#/definitions/value_is_child_of_predicate" - }, - { - "$ref": "#/definitions/value_is_unique" - }, - { - "$ref": "#/definitions/value_of_type" - }, - { - "$ref": "#/definitions/value_matches" - }, - { - "type": "string", - "enum": [ - "value_is_unique" - ] - } - ], - "default": null - }, - "notes": { - "type": "string", - "description": "Free text describing the rule applicable to this attribute" - } - } - }, - "scoped_semantic_rule": { - "type": "object", - "description": "A top-level rule expressing an expectation of attribute presence with optional constraints on its value", - "properties": { - "id": { - "type": "string", - "description": "A unique identifier for this rule" - }, - "path": { - "type": "string", - "description": "A top-down contextual path from the start of this document to the object being checked", - "pattern": "(/[^/]+)+", - "examples": [ - "/Library", - "/Library/Spectrum", - "/Library/Spectrum/Analyte" - ] - }, - "attr": { - "type": "array", - "items": { - "$ref": "#/definitions/semantic_attribute_rule" - } - }, - "combination_logic": { - "type": "string", - "enum": [ - "AND", - "OR", - "XOR" - ], - "default": "OR" - }, - "requirement_level": { - "type": "string", - "enum": [ - "MAY", - "SHOULD", - "MUST", - "REJECT" - ], - "default": "SHOULD" - }, - "condition": { - "$ref": "#/definitions/semantic_attribute_rule" - }, - "notes": { - "type": "string", - "description": "Free text describing this rule to a human reader" - } - } - } - } -} diff --git a/implementations/python/mzlib/validate/semantic_rule.py b/implementations/python/mzlib/validate/semantic_rule.py deleted file mode 100644 index 4d6f030..0000000 --- a/implementations/python/mzlib/validate/semantic_rule.py +++ /dev/null @@ -1,500 +0,0 @@ -import dataclasses -import io -import json -import logging -import re - -from datetime import datetime -from importlib import resources - -from xml.etree import ElementTree as etree - -from typing import Any, ClassVar, Dict, List, TYPE_CHECKING, Mapping, Optional, Sequence, Set, Tuple, Union - -from mzlib.attributes import Attributed -from mzlib.utils import flatten, ensure_iter -from mzlib.ontology import _VocabularyResolverMixin - -from .level import RequirementLevel, CombinationLogic - -if TYPE_CHECKING: - from .validator import ValidatorBase - - -logger = logging.getLogger(__name__) -logger.addHandler(logging.NullHandler()) - - -class AttributeSemanticPredicate: - name: ClassVar[str] - - _registry = {} - - def validate(self, attribute: 'AttributeSemanticRule', value: str, validator_context: "ValidatorBase") -> bool: - raise NotImplementedError() - - def to_dict(self) -> Dict[str, Any]: - raise NotImplementedError() - - @classmethod - def from_dict(cls, state: Dict[str, Any]) -> 'AttributeSemanticPredicate': - if isinstance(state, Mapping): - name = state['name'] - elif isinstance(state, str): - name = state - else: - raise TypeError(f"Cannot convert {state} to {cls.__name__}") - rule_tp = cls._registry[name] - return rule_tp.from_dict(state) - - def __init_subclass__(cls, *args, **kwargs): - cls._registry[cls.name] = cls - super().__init_subclass__(**kwargs) - - -class ValueOfType(AttributeSemanticPredicate): - type_name: Union[str, List[str]] - - name = "value_of_type" - - def __init__(self, type_name): - super().__init__() - self.type_name = type_name - - def validate(self, attribute: 'AttributeSemanticRule', value: str, validator_context: "ValidatorBase") -> bool: - if isinstance(value, list) and attribute.repeatable: - if all(self.validate(attribute, v, validator_context) for v in value): - return True - if not isinstance(self.type_name, list): - type_name = [self.type_name] - else: - type_name = self.type_name - result = False - for tp in type_name: - if tp == 'int': - result |= isinstance(value, int) or (isinstance(value, float) and value.is_integer()) - elif tp == 'float': - result |= isinstance(value, float) - elif tp == "string": - result |= isinstance(value, str) - elif tp == 'datetime': - if isinstance(value, datetime.datetime): - result |= True - elif isinstance(value, str): - logger.warning("Ambiguous datetime found for %s: %s", attribute, value) - result |= True - else: - raise ValueError(f"Can't validate type {tp}") - return result - - def to_dict(self) -> Dict[str, Any]: - return { - "name": self.name, - "type_name": self.type_name - } - - @classmethod - def from_dict(cls, state: Dict[str, Any]) -> 'AttributeSemanticPredicate': - return cls(state['type_name']) - - -class ValueIsChildOf(AttributeSemanticPredicate): - accession: str - - name = "value_is_child_of" - - def __init__(self, accession): - super().__init__() - self.accession = accession - - def validate(self, attribute: 'AttributeSemanticRule', value: str, validator_context: "ValidatorBase"): - if isinstance(value, list) and attribute.repeatable: - return all(self.validate(attribute, v, validator_context) for v in value) - for term in validator_context.walk_terms_for(self.accession): - if term == value: - if not term.startswith(self.accession): - return True - return False - - def to_dict(self) -> Dict[str, Any]: - return { - "name": self.name, - "accession": self.accession - } - - @classmethod - def from_dict(cls, state: Dict[str, Any]) -> 'AttributeSemanticPredicate': - return cls(state['accession']) - - -class ValueIsUnique(AttributeSemanticPredicate): - seen: set - - name = "value_is_unique" - - def __init__(self, *args, **kwargs): - super().__init__() - self.seen = set() - - def validate(self, attribute: 'AttributeSemanticRule', value: str, validator_context: "ValidatorBase"): - if isinstance(value, list): - if attribute.repeatable: - return all(self.validate(attribute, v, validator_context) for v in value) - else: - return False - if value in self.seen: - return False - self.seen.add(value) - return True - - def to_dict(self) -> Dict[str, Any]: - return { - "name": self.name, - } - - @classmethod - def from_dict(cls, state: Dict[str, Any]) -> 'AttributeSemanticPredicate': - return cls() - - -class ValueMatches(AttributeSemanticPredicate): - accession: str - - name = "value_matches" - - def __init__(self, accession): - super().__init__() - self.accession = accession - - def validate(self, attribute: 'AttributeSemanticRule', value: str, validator_context: "ValidatorBase"): - if isinstance(value, list) and attribute.repeatable: - return all(self.validate(attribute, v, validator_context) for v in value) - entity = validator_context.find_term_for(self.accession) - key = f"{entity.id}|{entity.name}" - return key == value - - def to_dict(self) -> Dict[str, Any]: - return { - "name": self.name, - "accession": self.accession - } - - @classmethod - def from_dict(cls, state: Dict[str, Any]) -> 'AttributeSemanticPredicate': - return cls(state['accession']) - - -class ValueMatchesPattern(AttributeSemanticPredicate): - pattern: re.Pattern - - name = "value_matches_pattern" - - def __init__(self, pattern: str): - super().__init__() - self.pattern = re.compile(pattern) - - def to_dict(self) -> Dict[str, Any]: - state = {} - state['name'] = self.name - state['pattern'] = self.pattern.pattern - return state - - @classmethod - def from_dict(cls, state: Dict[str, Any]) -> 'AttributeSemanticPredicate': - return cls(state['pattern']) - - -@dataclasses.dataclass(frozen=True) -class AttributeSemanticRule: - accession: str - name: str - repeatable: bool - allow_children: bool - value: Optional[AttributeSemanticPredicate] = dataclasses.field(default=None) - condition: Optional['AttributeSemanticRule'] = dataclasses.field(default=None) - notes: Optional[str] = dataclasses.field(default=None) - - @property - def attribute(self) -> str: - return f"{self.accession}|{self.name}" - - def to_dict(self) -> Dict[str, Any]: - state = { - "accession": self.accession, - "name": self.name, - "repeatable": self.repeatable, - "allow_children": self.allow_children, - } - if self.value is not None: - state['value'] = self.value.to_dict() - if self.condition is not None: - state['condition'] = self.condition.to_dict() - if self.notes: - state['notes'] = self.notes - return state - - @classmethod - def from_dict(cls, state, cv_provider: _VocabularyResolverMixin) -> 'AttributeSemanticRule': - if isinstance(state, str): - state = { - "accession": state, - } - - if "name" not in state: - term = cv_provider.find_term_for(state) - state['name'] = term.name - - repeatable = state.get("repeatable", False) - allow_children = state.get("allow_children", False) - - value_rule = state.get("value") - if value_rule: - value_rule = AttributeSemanticPredicate.from_dict(value_rule) - - condition = state.get("condition") - if condition: - condition = cls.from_dict(condition, cv_provider) - - attr_rule = cls( - state["accession"], - state["name"], - repeatable=repeatable, - allow_children=allow_children, - value=value_rule, - condition=condition, - notes=state.get('notes') - ) - return attr_rule - - -@dataclasses.dataclass -class ScopedSemanticRule: - id: str - path: str - attributes: List[AttributeSemanticRule] - requirement_level: RequirementLevel - combination_logic: CombinationLogic - condition: Optional[AttributeSemanticRule] = dataclasses.field(default=None) - notes: Optional[str] = dataclasses.field(default=None) - - def find_all_children_of(self, attribute_rule: AttributeSemanticRule, obj: Attributed, validator_context: "ValidatorBase") -> Tuple: - result = [] - for attrib in validator_context.walk_terms_for(attribute_rule.accession): - try: - hits = obj.get_attribute(attrib) - if hits is not None: - result.append((attrib, hits)) - except KeyError: - continue - return tuple(result) if result else None - - def check_rule(self, obj: Attributed, attrib: AttributeSemanticRule, validator_context: "ValidatorBase") -> bool: - result = True - if attrib.allow_children: - value = self.find_all_children_of(attrib, obj, validator_context) - else: - try: - value = obj.get_attribute(attrib.attribute) - except KeyError: - value = None - - if isinstance(value, list) and not attrib.repeatable: - result = False - if attrib.value: - if not attrib.value.validate(attrib, value, validator_context): - result = False - return result - - def validate(self, obj: Attributed, path: str, identifier_path: Tuple, validator_context: "ValidatorBase") -> bool: - values = [] - - if self.condition: - if not self.check_rule(obj, self.condition, validator_context): - return True - - for attrib in self.attributes: - if attrib.allow_children: - values.append(self.find_all_children_of(attrib, obj, validator_context)) - else: - try: - values.append(obj.get_attribute(attrib.attribute)) - except KeyError: - values.append(None) - - result = True - for attrib, value in zip(self.attributes, values): - # When `get_attribute` matches an attribute multiple times, this will be - # a list. `find_all_children_of` explicitly returns a tuple to avoid triggering - # this. - if isinstance(value, list) and not attrib.repeatable: - validator_context.add_warning( - obj, path, self, identifier_path, value, - self.requirement_level, - f"{attrib.attribute} cannot be repeated") - - result = False - if attrib.value: - if not attrib.value.validate(attrib, value, validator_context): - validator_context.add_warning( - obj, path, identifier_path, self, value, self.requirement_level, - f"{self.id} required the value of {attrib.accession}|{attrib.name} conform to {attrib.value.name}") - result = False - - has_value = [v is not None for v in values] - n_had_values = sum(has_value) - - if self.combination_logic == CombinationLogic.or_: - if n_had_values < 1: - validator_context.add_warning( - obj, path, identifier_path, self, value, self.requirement_level, - f"{self.id} requires one of {', '.join(attr.attribute for attr in self.attributes)}, none found") - result = False - - elif self.combination_logic == CombinationLogic.and_: - if n_had_values != len(self.attributes): - missing = [] - for attr, v in zip(self.attributes, has_value): - if not v: - missing.append(attr) - validator_context.add_warning( - obj, path, identifier_path, self, value, self.requirement_level, - f"{self.id} requires one of {', '.join(attr.attribute for attr in self.attributes)}, " - f"{', '.join(m.attribute for m in missing)} were absent") - result = False - - elif self.combination_logic == CombinationLogic.xor: - if n_had_values != 1: - validator_context.add_warning( - obj, path, identifier_path, self, value, self.requirement_level, - f"{self.id} requires exactly one of {', '.join(attr.attribute for attr in self.attributes)}, " - "multiple were found.") - result = False - return result - - def __call__(self, obj: Attributed, path: str, identifier_path: Tuple, validator_context: "ValidatorBase") -> bool: - return self.validate(obj, path, identifier_path, validator_context) - - @classmethod - def from_xml(cls, stream: io.IOBase) -> List['ScopedSemanticRule']: - tree = etree.parse(stream) - rules = [] - for node in tree.findall(".//CvMappingRule"): - term_rules = [] - for term in node.findall("CvTerm"): - term_rules.append( - AttributeSemanticRule( - term.attrib['termAccession'], - term.attrib['termName'], - repeatable=term.attrib['isRepeatable'] == 'true', - allow_children=term.attrib['allowChildren'] == 'true' - ) - ) - attrib = node.attrib - rule = ScopedSemanticRule( - id=attrib['id'], - path=attrib['scopePath'], - requirement_level=RequirementLevel.from_str(attrib['requirementLevel']), - combination_logic=CombinationLogic.from_str(attrib['cvTermsCombinationLogic']), - attributes=term_rules - ) - rules.append(rule) - return rules - - @classmethod - def from_dict(cls, data: Dict[str, Any], cv_provider: _VocabularyResolverMixin) -> List['ScopedSemanticRule']: - rules = [] - for rule_spec in data['rules']: - rule_id = rule_spec['id'] - level = RequirementLevel.from_str(rule_spec['level'].upper()) - path = rule_spec['path'] - combinator = CombinationLogic.from_str( - rule_spec.get("combination_logic", "OR").upper()) - - attribute_rules = [] - for attrib in rule_spec['attr']: - attr_rule = AttributeSemanticRule.from_dict(attrib, cv_provider) - attribute_rules.append(attr_rule) - - condition = rule_spec.get("condition") - if condition: - condition = AttributeSemanticRule.from_dict(condition, cv_provider) - - rules.append( - ScopedSemanticRule( - id=rule_id, - path=path, - attributes=attribute_rules, - requirement_level=level, - combination_logic=combinator, - condition=condition, - notes=rule_spec.get('rules') - ) - ) - return rules - - def to_dict(self) -> Dict[str, Any]: - state = { - "id": self.id, - "path": self.path, - "level": self.requirement_level.name.upper(), - "combination_logic": self.combination_logic.to_str(), - "attr": [ - a.to_dict() for a in self.attributes - ], - "notes": self.notes - } - if self.condition: - state['condition'] = self.condition - return state - - -class RuleSet(Sequence[ScopedSemanticRule]): - name: str - rules: List[ScopedSemanticRule] - - def __init__(self, name: str, rules: List[ScopedSemanticRule]): - super().__init__() - self.name = name - self.rules = rules - - def __iter__(self): - return iter(self.rules) - - def __len__(self): - return len(self.rules) - - def __getitem__(self, i): - return self.rules[i] - - @classmethod - def from_dict(cls, data: Dict[str, any]) -> 'RuleSet': - name = data['name'] - rules = ScopedSemanticRule.from_dict(data) - return cls(name, rules) - - def to_dict(self) -> Dict[str, Any]: - state = { - "name": self.name, - "rule": [ - rule.to_dict() for rule in self.rules - ] - } - return state - - -def load_rule_set(name: str) -> List[ScopedSemanticRule]: - res = resources.open_text( - __name__.replace(".semantic_rule", '') + '.rules', - name + '.json' - ) - - with res: - rules = ScopedSemanticRule.from_dict( - json.load(res), - _VocabularyResolverMixin() - ) - - return RuleSet( - name, - rules - ) diff --git a/implementations/python/mzlib/validate/validator.py b/implementations/python/mzlib/validate/validator.py deleted file mode 100644 index 1ec21cc..0000000 --- a/implementations/python/mzlib/validate/validator.py +++ /dev/null @@ -1,385 +0,0 @@ -import itertools -import logging -import warnings -import re -from dataclasses import dataclass, field -from typing import Any, Callable, Deque, Dict, Iterator, List, Optional, Sequence, Tuple, Union - -from psims.controlled_vocabulary.entity import Entity, ListOfType - -from mzlib.attributes import Attribute, Attributed - -from mzlib.spectrum import Spectrum -from mzlib.analyte import Analyte, Interpretation -from mzlib.spectrum_library import SpectrumLibrary - -from mzlib.ontology import _VocabularyResolverMixin - - -from mzlib.validate.level import RequirementLevel -from mzlib.validate.semantic_rule import ScopedSemanticRule, load_rule_set -from mzlib.validate.object_rule import ScopedObjectRuleBase, SpectrumPeakAnnotationRule, ValidationWarning -from mzlib.defaults import DEFAULT_UNITS - -logger = logging.getLogger(__name__) -logger.addHandler(logging.NullHandler()) - - -def walk_children(term: Entity): - queue = Deque([term]) - while queue: - term = queue.popleft() - yield term - queue.extend(term.children) - - -_is_curie = re.compile(r"(([A-Z]+):(.+))(?:\|.+)?") - -def is_curie(value: str) -> bool: - if isinstance(value, str): - return _is_curie.match(value) - return False - - -@dataclass -class ValidationContext: - attributes_visited: Dict[Tuple[str, str], bool] = field(default_factory=dict) - rule_states: Dict[str, Any] = field(default_factory=dict) - - def clear_attributes(self): - self.attributes_visited.clear() - - def record_attribute(self, attribute: Union[Tuple[str, str], Attribute], result: bool): - if isinstance(attribute, Attribute): - attribute = (attribute.key, attribute.group_id) - self.attributes_visited[attribute] = result - - def visited_attribute(self, attribute: Union[Tuple[str, str], Attribute]) -> bool: - if isinstance(attribute, Attribute): - attribute = (attribute.key, attribute.group_id) - return attribute in self.attributes_visited - - - -def _warning_iterator(iterator: Iterator[Spectrum]) -> Iterator[Spectrum]: - # coerce to an actual iterator in case we were passed only an iterable - iterator = iter(iterator) - while True: - try: - with warnings.catch_warnings(record=True) as w: - value = next(iterator) - vw = [a for a in w if issubclass(a.category, ValidationWarning)] - yield value, vw - except StopIteration: - break - except: - raise - - -def _is_of_type(attrib, relation) -> bool: - if isinstance(relation.value_type.type_definition, type): - return isinstance(attrib.value, relation.value_type.type_definition) - else: - return _try_convert(attrib.value, relation.value_type.type_definition) - - -def _try_convert(value, converter): - try: - converter(value) - return True - except (ValueError, TypeError): - return False - - -class ValidatorBase(_VocabularyResolverMixin): - error_log: List - current_context: ValidationContext - - def reset_context(self): - self.current_context.clear_attributes() - - def add_warning(self, obj: Attributed, path: str, identifier_path: Tuple, attrib: Any, value: Any, requirement_level: RequirementLevel, message: str): - raise NotImplementedError() - - def validate_spectrum(self, spectrum: Spectrum, path: str, library: SpectrumLibrary, parsing_warnings: Optional[List[warnings.WarningMessage]] = None): - raise NotImplementedError() - - def validate_analyte(self, analyte: Analyte, path: str, spectrum: Spectrum, library: SpectrumLibrary): - raise NotImplementedError() - - def validate_interpretation(self, interpretation: Interpretation, path: str, spectrum: Spectrum, library: SpectrumLibrary): - raise NotImplementedError() - - def apply_rules(self, obj: Attributed, path: str, identifier_path: Tuple) -> bool: - raise NotImplementedError() - - def check_attributes(self, obj: Attributed, path: str, identifer_path: Tuple) -> bool: - valid: bool = True - for attrib in obj.attributes: - if attrib.key == "MS:1003276|other attribute value" or attrib.key == "MS:1003275|other attribute name": - continue - if self.current_context.visited_attribute(attrib): - continue - try: - term = self.find_term_for(attrib.key.split("|")[0]) - except KeyError as err: - logger.warn(f"Could not resolve term for {attrib.key}") - continue - value_types = term.get('has_value_type') - if not value_types: - value_parsed = isinstance(attrib.value, Attribute) - if value_parsed or is_curie(attrib.value): - if value_parsed: - value_key = attrib.value.key.split("|")[0] - else: - value_key = attrib.value.split("|")[0] - if is_curie(value_key): - value_term = self.find_term_for(value_key) - else: - value_term = None - if not value_term or not value_term.is_of_type(term): - self.add_warning(obj, path, identifer_path, attrib.key, attrib.value, RequirementLevel.must, - f"The value type of {attrib.key} must be a term derived from {attrib.key}, but found {attrib.value}") - valid = False - continue - else: - self.add_warning(obj, path, identifer_path, attrib.key, attrib.value, RequirementLevel.must, - f"The value type of {attrib.key} must be a term derived from {attrib.key}") - valid = False - continue - else: - for rel in value_types: - if isinstance(rel.value_type, ListOfType): - hit = False - for tp in rel.value_type.type_definition.entity.has_value_type: - if isinstance(attrib.value, Sequence) and all(isinstance(v, tp.value_type.type_definition) for v in attrib.value): - hit = True - break - if hit: - break - elif _is_of_type(attrib, rel): - break - else: - self.add_warning(obj, path, identifer_path, attrib.key, attrib.value, RequirementLevel.must, - f"The value type of {attrib.key} must be a value of type {', '.join([rel.value_type.id for rel in value_types])}, but got {type(attrib.value)}") - valid = False - - units = term.get('has_units') - if units: - if not isinstance(units, list): - units = [units] - - if attrib.group_id is not None: - try: - unit_attrib = obj.get_attribute("UO:0000000|unit", group_identifier=attrib.group_id, raw=True) - except KeyError: - unit_attrib = None - if len(units) == 1: - logger.warning(f"{attrib.key}'s unit is missing, defaulting to {units[0]}") - continue - else: - unit_attrib = None - if len(units) == 1: - logger.warning(f"{attrib.key}'s unit is missing, defaulting to {units[0]}") - continue - if unit_attrib: - unit_acc, unit_name = unit_attrib.value.split("|", 1) - for unit in units: - if unit_acc == unit.accession or unit_name == unit.comment: - break - else: - self.add_warning(obj, path, identifer_path, attrib.key, attrib.value, RequirementLevel.must, - f"The attribute {attrib.key} must have a unit {', '.join([rel.accession + '|' + rel.comment for rel in units])}, but got {unit_acc}|{unit_name}") - valid = False - else: - if not term.id in DEFAULT_UNITS: - self.add_warning(obj, path, identifer_path, attrib.key, attrib.value, RequirementLevel.must, - f"The attribute {attrib.key} must have a unit {', '.join([rel.accession + '|' + rel.comment for rel in units])}, but none were found") - valid = False - - return valid - - def validate_library(self, library: SpectrumLibrary, spectrum_iterator: Optional[Iterator[Spectrum]]=None): - path = "/Library" - result = self.apply_rules(library, path, (library.identifier, )) - result &= self.check_attributes(library, path, (library.identifier, )) - self.reset_context() - - if spectrum_iterator is None: - spectrum_iterator = library - for spectrum, warns in _warning_iterator(spectrum_iterator): - result &= self.validate_spectrum(spectrum, path, library, parsing_warnings=warns) - return result - - def chain(self, validator: 'ValidatorBase') -> 'ValidatorBase': - return ValidatorChain([self, validator]) - - def __or__(self, other: 'ValidatorBase') -> 'ValidatorBase': - return self.chain(other) - - def walk_terms_for(self, curie: str) -> Iterator[str]: - term = self.find_term_for(curie) - for entity in walk_children(term): - yield f"{entity.id}|{entity.name}" - - -@dataclass -class ValidationError: - path: str - identifier_path: Tuple - attribute: Any - value: Any - requirement_level: RequirementLevel - message: str - - -class Validator(ValidatorBase): - name: str - semantic_rules: List[ScopedSemanticRule] - object_rules: List[ScopedObjectRuleBase] - - def __init__(self, name, semantic_rules: Optional[List[ScopedSemanticRule]] = None, object_rules: Optional[List[ScopedObjectRuleBase]] = None, error_log: Optional[List] = None): - super().__init__() - self.name = name - self.semantic_rules = semantic_rules or [] - self.object_rules = object_rules or [] - self.error_log = error_log or [] - self.current_context = ValidationContext() - - def apply_rules(self, obj: Attributed, path: str, identifier_path: Tuple) -> bool: - result = True - for rule in itertools.chain(self.semantic_rules, self.object_rules): - if rule.path == path: - v = rule(obj, path, identifier_path, self) - level = logging.DEBUG - if not v and rule.requirement_level > RequirementLevel.may: - level = logging.WARN - result &= v - logger.log(level, f"Applied {rule.id} to {path}:{identifier_path} {v}/{result}") - return result - - def validate_spectrum(self, spectrum: Spectrum, path: str, library: SpectrumLibrary, parsing_warnings: Optional[List[warnings.WarningMessage]] = None): - path = f"{path}/Spectrum" - identifier_path = (spectrum.key, ) - result = self.apply_rules(spectrum, path, identifier_path) - result &= self.check_attributes(spectrum, path, identifier_path) - self.reset_context() - - if parsing_warnings: - result = False - for parsing_warning in parsing_warnings: - logger.warn(str(parsing_warning.message)) - - for _key, analyte in spectrum.analytes.items(): - result &= self.validate_analyte(analyte, path, spectrum, library) - - for _key, interp in spectrum.interpretations.items(): - result &= self.validate_interpretation(interp, path, spectrum, library) - return result - - def validate_analyte(self, analyte: Analyte, path: str, spectrum: Spectrum, library: SpectrumLibrary): - path = f"{path}/Analyte" - identifier_path = (spectrum.key, analyte.id) - result = self.apply_rules(analyte, path, identifier_path) - result &= self.check_attributes(analyte, path, identifier_path) - self.reset_context() - return result - - def validate_interpretation(self, interpretation: Interpretation, path: str, spectrum: Spectrum, library: SpectrumLibrary): - path = f"{path}/Interpretation" - identifier_path = (spectrum.key, interpretation.id) - result = self.apply_rules(interpretation, path, identifier_path) - result &= self.check_attributes(interpretation, path, identifier_path) - self.reset_context() - return result - - def add_warning(self, obj: Attributed, path: str, identifier_path: Tuple, attrib: Any, value: Any, requirement_level: RequirementLevel, message: str): - if hasattr(obj, "key"): - key = obj.key - elif hasattr(obj, "id"): - key = obj.id - else: - key = '' - warning = f"{attrib.id if hasattr(attrib, 'id') else attrib} failed to validate {path}:{key} ({requirement_level.name.upper()}): {message}" - logger.warning(warning) - self.error_log.append(ValidationError(path, identifier_path, attrib, value, requirement_level, warning)) - - def __repr__(self): - return f"{self.__class__.__name__}({self.name!r}, {self.semantic_rules})" - - -class ValidatorChain(ValidatorBase): - validators: List[ValidatorBase] - - def __init__(self, validators: List[ValidatorBase], *args, **kwargs): - self.validators = list(validators) - super().__init__(*args, **kwargs) - - @property - def error_log(self): - log = [] - for validator in self.validators: - log.extend(validator.error_log) - return log - - def validate_spectrum(self, spectrum: Spectrum, path: str, library: SpectrumLibrary, parsing_warnings: Optional[List[warnings.WarningMessage]] = None): - result = True - for validator in self.validators: - result &= validator.validate_spectrum(spectrum, path, library, parsing_warnings) - return result - - def validate_analyte(self, analyte: Analyte, path: str, spectrum: Spectrum, library: SpectrumLibrary): - result = True - for validator in self.validators: - result &= validator.validate_analyte(analyte, path, spectrum, library) - return result - - def validate_interpretation(self, interpretation: Interpretation, path: str, spectrum: Spectrum, library: SpectrumLibrary): - result = True - for validator in self.validators: - result &= validator.validate_interpretation(interpretation, path, spectrum, library) - return result - - def apply_rules(self, obj: Attributed, path: str, identifier_path: Tuple) -> bool: - result = True - for validator in self.validators: - result &= validator.apply_rules(obj, path, identifier_path) - return result - - def check_attributes(self, obj: Attributed, path: str, identifer_path: Tuple) -> bool: - result = True - for validator in self.validators: - result &= validator.check_attributes(obj, path, identifer_path) - return result - - def reset_context(self): - for validator in self.validators: - validator.reset_context() - - def chain(self, validator: ValidatorBase) -> ValidatorBase: - self.validators.append(validator) - return self - - -predicates = { - "single_spectrum": lambda spec: spec.get_attribute("MS:1003065|spectrum aggregation type") == "MS:1003066|singleton spectrum", - "consensus_spectrum": lambda spec: spec.get_attribute("MS:1003065|spectrum aggregation type") == "MS:1003066|singleton spectrum", -} - - -object_rules = { - "peak_annotations": [SpectrumPeakAnnotationRule()] -} - - -def get_validator_for(name: str) -> Validator: - rules = load_rule_set(name) - validator = Validator(name, rules) - return validator - - -def get_object_validator_for(name: str) -> Validator: - rules = object_rules[name] - validator = Validator(name, object_rules=rules) - return validator - diff --git a/implementations/python/pyproject.toml b/implementations/python/pyproject.toml deleted file mode 100644 index 03961f9..0000000 --- a/implementations/python/pyproject.toml +++ /dev/null @@ -1,49 +0,0 @@ -[project] -name='mzlib' -version='0.1.0-alpha' -description='HUPO-PSI Spectral library format' -classifiers=[ - "Intended Audience :: Science/Research", - "Programming Language :: Python :: 3 :: Only", - "Topic :: Scientific/Engineering :: Bio-Informatics", - "Development Status :: 3 - Alpha" -] -dependencies = [ - "sqlalchemy", - "click", - "psims >= 0.1.41", - "pyteomics >= 4.5.3", - "mzpaf" -] - -[project.optional-dependencies] -test = [ - "jsonschema" -] -docs = [ - "sphinx", - "pydata-sphinx-theme", - "numpydoc>=1,<2", - "sphinx_click", - "myst-parser", - "sphinx-autobuild", -] - -[project.scripts] -mzspeclib = "mzlib.tools.cli:main" - -[build-system] -requires = ["setuptools"] -build-backend = "setuptools.build_meta" - -[tool.setuptools.packages] -find = {} - -[tool.ruff] -target-version = "py38" -line-length = 120 -select = ["D"] -ignore = ["D415", "D400", "D212", "D205", "D203", "D105"] - -[tool.ruff.pydocstyle] -convention = "numpy" diff --git a/implementations/python/setup.cfg b/implementations/python/setup.cfg deleted file mode 100644 index 6deafc2..0000000 --- a/implementations/python/setup.cfg +++ /dev/null @@ -1,2 +0,0 @@ -[flake8] -max-line-length = 120 diff --git a/implementations/python/tests/__init__.py b/implementations/python/tests/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/implementations/python/tests/common.py b/implementations/python/tests/common.py deleted file mode 100644 index 7658d87..0000000 --- a/implementations/python/tests/common.py +++ /dev/null @@ -1,14 +0,0 @@ -import os - -data_path = os.path.abspath( - os.path.join(os.path.dirname(__file__), "test_data")) - - -def datafile(name): - path = os.path.join(data_path, name) - if not os.path.exists(path): - raise Exception( - ("The path %r could not be located in the test suite's data package." % (path, )) + - "If you are NOT running the test suite, you should not" - " be using this function.") - return path diff --git a/implementations/python/tests/test_cluster.py b/implementations/python/tests/test_cluster.py deleted file mode 100644 index a4a3047..0000000 --- a/implementations/python/tests/test_cluster.py +++ /dev/null @@ -1,21 +0,0 @@ -import os -import unittest - -from mzlib.backends import TextSpectralLibrary -from mzlib.cluster import SpectrumCluster - -from .common import datafile - - -class TestSpectrumCluster(unittest.TestCase): - - def get_library(self): - test_file = datafile("clusters_example.mzlb") - return TextSpectralLibrary(test_file) - - def test_text_cluster_parsing(self): - lib = self.get_library() - cluster: SpectrumCluster = lib.get_cluster(1) - - assert cluster.key == 1 - assert cluster.size == 6 \ No newline at end of file diff --git a/implementations/python/tests/test_data/annotations.txt b/implementations/python/tests/test_data/annotations.txt deleted file mode 100644 index f7472a2..0000000 --- a/implementations/python/tests/test_data/annotations.txt +++ /dev/null @@ -1,419 +0,0 @@ -? -IF/0.2ppm -IK+i/4.4ppm -IK/-0.3ppm -IK/0.5ppm -IR/-0.3ppm -IR/-1.4ppm -IR/-2.6ppm -IR/0.7ppm -IR/2.0ppm -a2+i/5.4ppm -a2/-0.8ppm -a2/-1.6ppm -a4+i/7.9ppm -a4/-0.8ppm -a4/-1.2ppm -a4/0.3ppm -a4/1.5ppm -a4/3.8ppm -a4/9.7ppm -a5+i/-0.6ppm -a5/-2.8ppm -a5/1.3ppm -a5/1.7ppm -a5/3.9ppm -a6/-1.4ppm -a6/-2.9ppm -a6/12.5ppm -a6/16.6ppm -a7/-1.7ppm -a7/0.8ppm -a7/3.6ppm -a8+i/2.7ppm -a8/1.3ppm -a9/0.9ppm -b11/-16.6ppm -b13-H2O/1.1ppm -b14+i/10.2ppm -b14-H2O/2.9ppm -b14-H2O^2/1.7ppm -b14/1.3ppm -b2+i/4.2ppm -b2+i/5.6ppm -b2/-0.7ppm -b2/0.0ppm -b2/0.7ppm -b2/5.6ppm -b3+i/-4.2ppm -b3+i/2.3ppm -b3+i/4.2ppm -b3+i/4.6ppm -b3/-0.5ppm -b3/0.4ppm -b3/0.9ppm -b3/1.3ppm -b3/4.1ppm -b4+i/3.8ppm -b4+i/4.8ppm -b4/-0.1ppm -b4/-0.5ppm -b4/-0.8ppm -b4/0.9ppm -b4/2.0ppm -b4/3.4ppm -b4/4.5ppm -b5+i/-5.6ppm -b5+i/6.6ppm -b5-NH2-CO-CH2SH+i/-1.9ppm -b5-NH2-CO-CH2SH/-0.8ppm 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dissociation -[2]MS:1000045|collision energy=46 -[2]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=5538 -MS:1003203|constituent spectrum file="CHO-K1_bRPLC_C1.RAW.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=2 -MS:1000002|sample name="jhu_cho_brplc_cam" -MS:1003079|total unassigned intensity fraction=0.2848 -MS:1003080|top 20 peak unassigned intensity fraction=0.1879 -MS:1000028|detector resolution=7500 -[3]MS:1000828|isolation window lower offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -[4]MS:1000829|isolation window upper offset=0.95 -[4]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=8799173.32 -MS:1003086|precursor apex intensity=25273307.5 -MS:1000512|filter string="FTMS + p NSI d Full ms2 855.96@hcd35.00 [140.00-1725.00]" -MS:1003059|number of peaks=87 -[5]MS:1003275|other attribute name=Se -[5]MS:1003276|other attribute value=1(^G1:sc=8.13346e-015) 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-201.7527 5576.3 ? -212.1051 13786.1 ? -214.1195 82269.8 b3/4.1ppm -229.1552 7852.0 ? -232.0764 28555.9 ? -249.1071 4670.7 ? -257.1633 15001.9 a4/9.7ppm -276.4497 5288.0 ? -283.1411 24965.9 ? -283.3943 5090.5 ? -285.1567 48285.5 b4/3.4ppm -302.1834 10558.9 ? -303.114 52736.6 ? -317.1891 6585.3 y3/-12.9ppm -345.1593 18050.6 ? -354.1793 31400.1 b5-NH2-CO-CH2SH/5.9ppm -356.1916 7124.1 ? -370.3776 6139.7 ? -371.6662 11983.3 ? -374.1505 34930.7 ? -416.2029 8953.6 ? -417.1931 16940.5 a5/3.9ppm -425.2171 15449.8 b6-NH2-CO-CH2SH/6.6ppm -428.2024 8874.5 m-1:8-H2O/14.4ppm -428.249 6831.1 ? -430.278 30118.6 y4/1.8ppm -445.1886 57883.2 b5/5.0ppm -446.2049 8868.2 m5:8/-4.2ppm -457.1753 5403.5 ? -467.2682 6117.4 ? -469.2735 6906.4 ? -471.2018 9435.3 ? -487.2299 15480.3 ? -488.2367 13813.7 a6/16.6ppm -490.7795 12739.9 y10^2/-0.6ppm -491.2839 6651.0 y10+i^2/5.4ppm -495.9153 6370.5 ? -499.2364 5273.9 m4:8-H2O/6.2ppm -516.2236 49862.4 b6/0.2ppm -528.2323 9881.3 ? -530.2752 10333.1 ? -541.3164 7041.3 ? -545.308 6833.8 y5/7.0ppm -558.2726 23958.7 ? -570.3232 6006.3 ? -601.3148 11919.6 a7/3.6ppm -617.2834 5841.2 ? -617.3372 4342.1 ? -629.3052 22419.3 b7/-3.7ppm -641.3058 11147.2 m2:8-H2O/-2.7ppm -659.3259 9164.2 m2:8/11.8ppm -685.3383 6861.0 ? -712.3472 13798.2 b8-H2O/3.6ppm -730.3578 16426.3 b8/3.5ppm -826.4765 18892.5 y8/-2.0ppm -855.017 7062.7 ? -855.5167 249849.0 ? -856.523 57946.3 ? -883.4993 29383.7 y9/-0.3ppm -922.4447 6413.2 ? -934.4906 6605.4 ? -963.5431 13545.1 y10-NH3/17.9ppm -980.556 559065.0 y10/3.7ppm -981.5587 216762.0 y10+i/3.6ppm -1037.5859 14218.2 ? -1038.5812 9574.2 ? -1067.8983 6611.6 ? -1081.6041 179858.0 y11/3.8ppm -1082.6077 79540.9 y11+i/4.5ppm -1143.0283 6099.8 ? -1194.6899 106907.0 y12/4.9ppm -1195.6869 50339.1 y12+i/-0.1ppm -1265.7273 83029.7 y13/4.8ppm -1266.7281 42164.7 y13+i/3.2ppm -1390.1328 5531.5 ? -1395.6904 8549.2 ? -1425.7538 51400.1 y14/1.4ppm -1426.7601 40643.8 y14+i/3.8ppm -1496.7792 11918.3 q15/-6.5ppm - - -MS:1003061|library spectrum name=AAAACALTPGPLADLAAR/2_1(4,C,CAM)_46eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1000041|charge state=2 -MS:1000744|selected ion m/z=855.4538 -[1]MS:1001975|delta m/z=1.4 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[2]MS:1000045|collision energy=46 -[2]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=5538 -MS:1003203|constituent spectrum file="CHO-K1_bRPLC_C1.RAW.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=2 -MS:1000002|sample name="jhu_cho_brplc_cam" -MS:1003079|total unassigned intensity fraction=0.2848 -MS:1003080|top 20 peak unassigned intensity fraction=0.1879 -MS:1000028|detector resolution=7500 -[3]MS:1000828|isolation window lower offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -[4]MS:1000829|isolation window upper offset=0.95 -[4]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=8799173.32 -MS:1003086|precursor apex intensity=25273307.5 -MS:1000512|filter string="FTMS + p NSI d Full ms2 855.96@hcd35.00 [140.00-1725.00]" -MS:1003059|number of peaks=87 -[5]MS:1003275|other attribute name=Se -[5]MS:1003276|other attribute value=1(^G1:sc=8.13346e-015) -[6]MS:1003275|other attribute name=max_unassigned_ab -[6]MS:1003276|other attribute value=0.45 -[7]MS:1003275|other attribute name=num_unassigned_peaks -[7]MS:1003276|other attribute value=4/20 - -MS:1000224|molecular mass=1710.9076 -[1]MS:1003048|number of enzymatic termini=2 -[1]MS:1001045|cleavage agent name=MS:1001251|Trypsin -MS:1001471|peptide modification details=1(4,C,CAM) -MS:1000888|stripped peptide sequence=AAAACALTPGPLADLAAR -MS:1001112|n-terminal flanking residue=R -MS:1001113|c-terminal flanking residue=L -MS:1000885|protein accession="tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1" -MS:1003053|theoretical monoisotopic m/z=855.455 -MS:1003169|proforma peptidoform sequence=AAAAC[Carbamidomethyl]ALTPGPLADLAAR - - -143.0823 14791.5 b2/5.6ppm -153.2575 5008.6 ? -159.0917 11531.8 ? -162.5977 5804.6 ? -169.0972 12931.0 ? -175.1193 18211.1 y1/2.0ppm,IR/2.0ppm -194.0699 6011.0 ? -199.1074 6737.4 ? -201.7527 5576.3 ? -212.1051 13786.1 ? -214.1195 82269.8 b3/4.1ppm -229.1552 7852.0 ? -232.0764 28555.9 ? -249.1071 4670.7 ? -257.1633 15001.9 a4/9.7ppm -276.4497 5288.0 ? -283.1411 24965.9 ? -283.3943 5090.5 ? -285.1567 48285.5 b4/3.4ppm -302.1834 10558.9 ? -303.114 52736.6 ? -317.1891 6585.3 y3/-12.9ppm -345.1593 18050.6 ? -354.1793 31400.1 b5-NH2-CO-CH2SH/5.9ppm -356.1916 7124.1 ? -370.3776 6139.7 ? -371.6662 11983.3 ? -374.1505 34930.7 ? -416.2029 8953.6 ? -417.1931 16940.5 a5/3.9ppm -425.2171 15449.8 b6-NH2-CO-CH2SH/6.6ppm -428.2024 8874.5 m-1:8-H2O/14.4ppm -428.249 6831.1 ? -430.278 30118.6 y4/1.8ppm -445.1886 57883.2 b5/5.0ppm -446.2049 8868.2 m5:8/-4.2ppm -457.1753 5403.5 ? -467.2682 6117.4 ? -469.2735 6906.4 ? -471.2018 9435.3 ? -487.2299 15480.3 ? -488.2367 13813.7 a6/16.6ppm -490.7795 12739.9 y10^2/-0.6ppm -491.2839 6651.0 y10+i^2/5.4ppm -495.9153 6370.5 ? -499.2364 5273.9 m4:8-H2O/6.2ppm -516.2236 49862.4 b6/0.2ppm -528.2323 9881.3 ? -530.2752 10333.1 ? -541.3164 7041.3 ? -545.308 6833.8 y5/7.0ppm -558.2726 23958.7 ? -570.3232 6006.3 ? -601.3148 11919.6 a7/3.6ppm -617.2834 5841.2 ? -617.3372 4342.1 ? -629.3052 22419.3 b7/-3.7ppm -641.3058 11147.2 m2:8-H2O/-2.7ppm -659.3259 9164.2 m2:8/11.8ppm -685.3383 6861.0 ? -712.3472 13798.2 b8-H2O/3.6ppm -730.3578 16426.3 b8/3.5ppm -826.4765 18892.5 y8/-2.0ppm -855.017 7062.7 ? -855.5167 249849.0 ? -856.523 57946.3 ? -883.4993 29383.7 y9/-0.3ppm -922.4447 6413.2 ? -934.4906 6605.4 ? -963.5431 13545.1 y10-NH3/17.9ppm -980.556 559065.0 y10/3.7ppm -981.5587 216762.0 y10+i/3.6ppm -1037.5859 14218.2 ? -1038.5812 9574.2 ? -1067.8983 6611.6 ? -1081.6041 179858.0 y11/3.8ppm -1082.6077 79540.9 y11+i/4.5ppm -1143.0283 6099.8 ? -1194.6899 106907.0 y12/4.9ppm -1195.6869 50339.1 y12+i/-0.1ppm -1265.7273 83029.7 y13/4.8ppm -1266.7281 42164.7 y13+i/3.2ppm -1390.1328 5531.5 ? -1395.6904 8549.2 ? -1425.7538 51400.1 y14/1.4ppm -1426.7601 40643.8 y14+i/3.8ppm -1496.7792 11918.3 q15/-6.5ppm \ No newline at end of file diff --git a/implementations/python/tests/test_data/chinese_hamster_hcd_selected_head.msp b/implementations/python/tests/test_data/chinese_hamster_hcd_selected_head.msp deleted file mode 100644 index 6e735cd..0000000 --- a/implementations/python/tests/test_data/chinese_hamster_hcd_selected_head.msp +++ /dev/null @@ -1,1000 +0,0 @@ -Name: AAAACALTPGPLADLAAR/2_1(4,C,CAM)_46eV -MW: 1710.9076 -Comment: Single Pep=Tryptic Mods=1(4,C,CAM) Fullname=R.AAAACALTPGPLADLAAR.L Charge=2 Parent=855.4538 Se=1(^G1:sc=8.13346e-015) Mz_diff=1.4ppm HCD=46eV Scan=5538 Origfile="CHO-K1_bRPLC_C1.RAW.FT.hcd.ch.MGF" Nreps=1/2 Sample="jhu_cho_brplc_cam" Protein="tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1" Unassign_all=0.2848 Unassigned=0.1879 max_unassigned_ab=0.45 num_unassigned_peaks=4/20 FTResolution=7500 ms2IsolationWidth=1.90 ms1PrecursorAb=8799173.32 Precursor1MaxAb=25273307.50 PrecursorMonoisoMZ=855.4550 Filter="FTMS + p NSI d Full ms2 855.96@hcd35.00 [140.00-1725.00]" -Num peaks: 87 -143.0823 14791.5 "b2/5.6ppm" -153.2575 5008.6 "?" -159.0917 11531.8 "?" -162.5977 5804.6 "?" -169.0972 12931 "?" -175.1193 18211.1 "y1/2.0ppm,IRJ/2.0ppm" -194.0699 6011 "?" -199.1074 6737.4 "?" -201.7527 5576.3 "?" -212.1051 13786.1 "?" -214.1195 82269.8 "b3/4.1ppm" -229.1552 7852 "?" -232.0764 28555.9 "?" -249.1071 4670.7 "?" -257.1633 15001.9 "a4/9.7ppm" -276.4497 5288 "?" -283.1411 24965.9 "?" -283.3943 5090.5 "?" -285.1567 48285.5 "b4/3.4ppm" -302.1834 10558.9 "?" -303.114 52736.6 "?" -317.1891 6585.3 "y3/-12.9ppm" -345.1593 18050.6 "?" -354.1793 31400.1 "b5-NH2-CO-CH2SH/5.9ppm" -356.1916 7124.1 "?" -370.3776 6139.7 "?" -371.6662 11983.3 "?" -374.1505 34930.7 "?" -416.2029 8953.6 "?" -417.1931 16940.5 "a5/3.9ppm" -425.2171 15449.8 "b6-NH2-CO-CH2SH/6.6ppm" -428.2024 8874.5 "Int/cALT-H2O/14.4ppm" -428.249 6831.1 "?" -430.278 30118.6 "y4/1.8ppm" -445.1886 57883.2 "b5/5.0ppm" -446.2049 8868.2 "Int/cALT/-4.2ppm" -457.1753 5403.5 "?" -467.2682 6117.4 "?" -469.2735 6906.4 "?" -471.2018 9435.3 "?" -487.2299 15480.3 "?" -488.2367 13813.7 "a6/16.6ppm" -490.7795 12739.9 "y10^2/-0.6ppm" -491.2839 6651 "y10^2+i/5.4ppm" -495.9153 6370.5 "?" -499.2364 5273.9 "Int/AcALT-H2O/6.2ppm" -516.2236 49862.4 "b6/0.2ppm" -528.2323 9881.3 "?" -530.2752 10333.1 "?" -541.3164 7041.3 "?" -545.308 6833.8 "y5/7.0ppm" -558.2726 23958.7 "?" -570.3232 6006.3 "?" -601.3148 11919.6 "a7/3.6ppm" -617.2834 5841.2 "?" -617.3372 4342.1 "?" -629.3052 22419.3 "b7/-3.7ppm" -641.3058 11147.2 "Int/AAAcALT-H2O/-2.7ppm" -659.3259 9164.2 "Int/AAAcALT/11.8ppm" -685.3383 6861 "?" -712.3472 13798.2 "b8-H2O/3.6ppm" -730.3578 16426.3 "b8/3.5ppm" -826.4765 18892.5 "y8/-2.0ppm" -855.017 7062.7 "?" -855.5167 249849 "?" -856.523 57946.3 "?" -883.4993 29383.7 "y9/-0.3ppm" -922.4447 6413.2 "?" -934.4906 6605.4 "?" -963.5431 13545.1 "y10-NH3/17.9ppm" -980.556 559065 "y10/3.7ppm" -981.5587 216762 "y10+i/3.6ppm" -1037.5859 14218.2 "?" -1038.5812 9574.2 "?" -1067.8983 6611.6 "?" -1081.6041 179858 "y11/3.8ppm" -1082.6077 79540.9 "y11+i/4.5ppm" -1143.0283 6099.8 "?" -1194.6899 106907 "y12/4.9ppm" -1195.6869 50339.1 "y12+i/-0.1ppm" -1265.7273 83029.7 "y13/4.8ppm" -1266.7281 42164.7 "y13+i/3.2ppm" -1390.1328 5531.5 "?" -1395.6904 8549.2 "?" -1425.7538 51400.1 "y14/1.4ppm" -1426.7601 40643.8 "y14+i/3.8ppm" -1496.7792 11918.3 "y15/-6.5ppm" - -Name: AAAACALTPGPLADLAAR/2_1(4,C,CAM)_53eV -MW: 1710.9076 -Comment: Single Pep=Tryptic Mods=1(4,C,CAM) Fullname=R.AAAACALTPGPLADLAAR.L Charge=2 Parent=855.4538 Se=1(^G1:sc=1.31932e-020) Mz_diff=4.2ppm HCD=53eV Scan=6275 Origfile="RO-QC-141112_Betenbaugh_HK_Fraction46.raw.FT.hcd.ch.MGF" Nreps=1/14 Sample="betenbaugh_hk2" Protein="tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1" Unassign_all=0.3165 Unassigned=0.1420 max_unassigned_ab=0.16 num_unassigned_peaks=5/20 FTResolution=15000 ms2IsolationWidth=1.90 ms1PrecursorAb=1776618.56 Precursor1MaxAb=12167259.65 PrecursorMonoisoMZ=855.4574 Filter="FTMS + p NSI d Full ms2 855.95@hcd35.00 [140.00-1725.00]" -Num peaks: 204 -143.0814 9555.6 "b2/-0.7ppm" -169.097 5174.5 "?" -171.1126 2428.2 "?" -175.1069 1175.7 "?" -175.1187 7806.9 "y1/-1.4ppm,IRJ/-1.4ppm" -178.0645 645.1 "?" -181.0971 2623.7 "?" -183.1495 1770.8 "Int/PL-CO/1.7ppm" -185.0921 4004 "?" -185.1288 983.4 "Int/LA/1.9ppm" -199.1073 2854.3 "?" -203.1022 2225.3 "?" -203.412 489.7 "?" -204.0803 4532 "?" -211.1438 1671.5 "Int/PL/-1.4ppm" -212.103 6959.1 "y2-2NH3/0.2ppm" -214.1185 23984.8 "b3/-0.5ppm" -215.0481 1035.3 "?" -215.1219 1943.5 "b3+i/2.3ppm" -215.1392 1652.7 "Int/LT/0.8ppm" -216.0967 632.6 "?" -229.1299 970.3 "y2-NH3/1.7ppm" -231.1446 601.8 "?" -232.0748 11826.6 "?" -235.1929 547.3 "?" -240.1344 3195.6 "?" -242.1137 1025.5 "?" -246.1558 1514.8 "y2/-1.1ppm" -255.1454 790.9 "?" -256.1652 1376.9 "?" -257.1605 3523.6 "a4/-1.2ppm" -258.0901 1119.1 "?" -268.1656 1623.7 "Int/ALT-H2O/0.1ppm" -282.1807 1542.2 "Int/PLA/-1.8ppm" -283.14 10639.1 "?" -284.1443 1021 "?" -285.1555 11955.3 "b4/-0.8ppm" -286.1599 1072.8 "b4+i/4.8ppm" -286.1761 2533.2 "Int/ALT/-0.1ppm" -293.366 528.7 "?" -298.177 1429.9 "?" -302.1818 2634.5 "?" -303.1121 15782.5 "?" -304.1151 1344.9 "?" -309.1558 945 "?" -311.1712 2335.2 "?" -317.1934 2115 "y3/0.7ppm" -327.2036 961.2 "?" -328.1647 1131.6 "?" -329.1273 3077.6 "?" -331.1088 859.4 "?" -337.2232 2252 "Int/PGPL-CO/-0.6ppm" -339.2033 1220.8 "?" -341.1834 794.7 "?" -345.1589 6582.2 "?" -346.1541 1361.2 "?" -353.2189 1800 "?" -354.1769 9317.5 "b5-NH2-CO-CH2SH/-0.8ppm" -355.1793 1293.7 "b5-NH2-CO-CH2SH+i/-1.9ppm" -356.1933 1800.3 "?" -357.211 686.5 "?" -358.2065 618.4 "?" -363.3883 563.8 "?" -365.2181 2776.2 "y7^2/4.9ppm" -366.2212 705.5 "?" -368.1942 682 "?" -369.3904 685.6 "?" -370.4914 4171.5 "?" -372.1714 835.1 "?" -374.149 10475.6 "?" -375.153 1112.5 "?" -380.1929 960.8 "?" -384.1859 584.6 "?" -386.2027 978.1 "?" -396.2243 975.1 "?" -397.2071 1560.8 "Int/PLAD/-2.7ppm" -398.2401 1130.2 "?" -400.1644 4875.2 "?" -401.1676 730.6 "?" -402.1434 1170.3 "?" -408.2588 885.8 "Int/PGPLA-CO/-4.2ppm" -410.2415 678.5 "?" -416.1944 2264.1 "?" -417.192 3203.6 "a5/1.3ppm" -418.1938 714.5 "a5+i/-0.6ppm" -422.2396 762.6 "?" -425.2144 2490.8 "b6-NH2-CO-CH2SH/0.2ppm" -428.1953 1647.7 "Int/cALT-H2O/-2.1ppm" -430.2767 20600 "y4/-1.3ppm" -431.2812 3236 "y4+i/2.9ppm" -436.2548 3128.6 "Int/PGPLA/-1.5ppm" -442.2117 1223.9 "?" -445.1862 10843.9 "b5/-0.4ppm" -446.1865 1519 "b5+i/-5.6ppm" -446.2101 1269.8 "Int/cALT/7.4ppm" -454.23 854.8 "?" -459.2378 1549.6 "?" -471.2021 2150.3 "?" -473.1871 733.9 "?" -474.2351 776.1 "?" -487.2318 3002.2 "?" -488.2279 2861.1 "a6/-1.4ppm" -490.7802 1998.5 "y10^2/0.8ppm" -493.2748 802.6 "?" -499.2884 798.8 "?" -505.2755 1577.1 "?" -513.2489 2142.4 "?" -516.223 7108.2 "b6/-1.0ppm" -517.22 1175.7 "b6+i/-11.9ppm" -528.2206 1033.3 "?" -528.2757 1044.1 "y5-NH3/-3.7ppm" -530.2791 1202.4 "?" -533.272 1261.5 "?" -535.1867 572.4 "?" -543.2589 744.4 "?" -545.3041 3290.4 "y5/-0.2ppm" -546.2418 626 "?" -546.3103 815.6 "y5+i/6.2ppm" -551.2829 4018.4 "Int/PGPLAD/0.9ppm" -552.287 815.2 "Int/PGPLAD+i/3.0ppm" -558.2695 4055.3 "?" -559.2736 821.5 "?" -570.2687 978.2 "Int/AAcALT-H2O/-3.1ppm" -588.277 1266.6 "Int/AAcALT/-6.8ppm" -601.3116 1037.7 "a7/-1.7ppm" -609.3334 1558.5 "?" -616.3435 2514.4 "y6/3.6ppm" -629.3079 1030.1 "b7/0.5ppm" -636.3726 1099.2 "Int/PGPLADL-CO/1.7ppm" -638.3498 623.7 "?" -641.3058 1372.7 "Int/AAAcALT-H2O/-2.7ppm" -659.3138 896.8 "Int/AAAcALT/-6.6ppm" -664.3644 2215.2 "Int/PGPLADL/-3.1ppm" -665.3702 616.9 "Int/PGPLADL+i/1.2ppm" -698.652 964.9 "?" -710.8712 676.6 "?" -712.343 766.7 "b8-H2O/-2.3ppm" -728.644 669.7 "?" -729.4229 1339.5 "y7/-3.4ppm" -730.3568 859 "b8/2.1ppm" -735.4047 1839.2 "Int/PGPLADLA/1.5ppm" -735.7518 597 "?" -736.4097 726.4 "b9-NH2-CO-CH2SH/14.8ppm,Int/PGPLADLA+i/4.3ppm" -758.5785 584.4 "?" -804.5634 599.5 "?" -806.4404 871.1 "Int/PGPLADLAA/-0.3ppm" -807.4396 706.8 "Int/PGPLADLAA+i/-5.0ppm" -809.4468 1047 "y8-NH3/-5.9ppm" -826.4767 5889.7 "y8/-1.7ppm" -827.4818 1704.1 "y8+i/1.0ppm" -835.4305 6503.5 "?" -836.4305 855.7 "?" -855.5272 1972.3 "?" -883.499 11027.3 "y9/-0.7ppm" -884.5011 4136.3 "y9+i/-1.5ppm" -920.521 899.9 "?" -922.4631 6661.9 "?" -923.4683 1004.4 "?" -938.5323 694.4 "?" -954.0876 657.8 "?" -962.5461 1056.8 "y10-H2O/4.5ppm" -963.5266 5559.2 "y10-NH3/0.8ppm" -964.5276 3037.9 "y10-NH3+i/-1.1ppm" -980.5516 101168 "y10/-0.8ppm" -981.5547 48825.1 "y10+i/-0.5ppm" -982.556 3169.3 "y10+2i/-1.8ppm" -998.153 653.4 "?" -1026.4183 641.1 "?" -1033.4918 1042.9 "?" -1037.5729 7440.8 "?" -1038.5754 4253.3 "?" -1050.5208 5312.6 "?" -1063.5883 1995.7 "y11-H2O/-1.1ppm" -1064.5804 1437.3 "y11-NH3/6.5ppm,y11-H2O+i/-11.2ppm" -1081.5985 28537.7 "y11/-1.4ppm" -1082.6017 16194.1 "y11+i/-1.1ppm" -1083.5983 1228.4 "y11+2i/-6.6ppm" -1150.6531 1305.7 "?" -1176.6824 1518.9 "y12-H2O/7.5ppm" -1177.6671 1170.1 "y12-NH3/8.1ppm,y12-H2O+i/-7.9ppm" -1182.254 639.1 "?" -1194.6826 20850.2 "y12/-1.3ppm" -1195.6853 12324.9 "y12+i/-1.4ppm" -1197.5858 4604.9 "?" -1221.6934 1065.9 "?" -1247.7007 1013.5 "y13-H2O/-8.0ppm" -1252.6328 702.9 "?" -1265.7198 16380.4 "y13/-1.1ppm" -1266.7246 9779.2 "y13+i/0.4ppm" -1267.7239 747.9 "y13+2i/-2.2ppm" -1298.6331 3899.6 "?" -1334.7629 576.6 "y14-NH2-CO-CH2SH/15.2ppm" -1395.6888 9418.6 "?" -1396.6947 2451.5 "?" -1407.7356 1083.1 "y14-H2O/-4.0ppm" -1408.7473 1011.7 "y14-NH3/15.6ppm,y14-H2O+i/2.3ppm" -1425.7515 7609.8 "y14/-0.3ppm" -1426.7562 7554 "y14+i/1.1ppm" -1466.0739 798.5 "?" -1495.1215 635.8 "?" -1496.7932 1534.6 "y15/2.8ppm" -1497.7944 1455 "y15+i/1.7ppm" -1557.3423 600.8 "?" -1628.3004 719.6 "?" - -Name: AAAAGQTGTVPPGAPGALPLPGMAIVK/2_0_76eV -MW: 2414.3344 -Comment: Single Pep=SemiTryptic Mods=0 Fullname=A.AAAAGQTGTVPPGAPGALPLPGMAIVK.E Charge=2 Parent=1207.1672 Se=1(^G1:sc=1.43642e-012) Mz_diff=-0.9ppm HCD=76eV Scan=7528 Origfile="RO-QC-141112_Betenbaugh_HK_Fraction18.raw.FT.hcd.ch.MGF" Nreps=1/2 Sample="betenbaugh_hk1" Protein="tr|G3I2Q7|G3I2Q7_CRIGR Transcription intermediary factor 1-beta OS=Cricetulus griseus GN=I79_017700 PE=4 SV=1" Unassign_all=0.2591 Unassigned=0.0000 max_unassigned_ab=0.12 num_unassigned_peaks=0/20 FTResolution=15000 ms2IsolationWidth=1.90 ms1PrecursorAb=6939079.20 Precursor1MaxAb=7583304.35 PrecursorMonoisoMZ=1207.1661 Filter="FTMS + p NSI d Full ms2 1207.67@hcd35.00 [140.00-2000.00]" -Num peaks: 122 -143.0816 2935.3 "b2/0.7ppm" -147.1127 2210.5 "y1/-0.7ppm" -154.4137 1587.1 "?" -155.0816 2825.2 "Int/PG/0.6ppm" -169.771 1665.2 "?" -176.5942 1535.3 "?" -181.0984 2034.3 "?" -186.0873 2509.4 "?" -198.5815 1458.2 "?" -199.2009 1692.3 "?" -206.924 1799.6 "?" -214.1185 6874.5 "b3/-0.5ppm" -214.6242 1695 "?" -216.197 1659.5 "?" -224.6321 1496.3 "?" -226.1183 6292.8 "Int/PGA/-1.4ppm" -227.4689 1609.1 "?" -230.1134 2157.9 "?" -240.1377 1613.7 "?" -246.1817 2500.8 "y2/2.0ppm" -252.1353 2976.9 "Int/PPG/4.1ppm" -257.1249 2901.5 "?" -257.1618 2468.8 "a4/3.8ppm" -266.3697 1813.9 "?" -283.6819 1747.3 "?" -285.1557 5707.9 "b4/-0.1ppm" -285.8154 1730.9 "?" -287.1343 2200.9 "?" -295.139 1768.2 "?" -295.1769 3116.9 "Int/PGAP-CO/1.5ppm,Int/PPGA-CO/1.5ppm" -323.1715 9768.4 "Int/PGAP/0.4ppm,Int/PPGA/0.4ppm" -326.1471 1541 "?" -328.1606 3372.4 "?" -339.2022 4142.5 "Int/PGAL/-1.4ppm" -342.1785 2123.8 "b5/3.8ppm" -357.1593 8559.3 "Int/PGMA/0.6ppm" -368.2019 1424.3 "?" -370.1709 2286.1 "?" -382.171 2478.3 "?" -399.199 2560.8 "?" -404.719 1744.2 "?" -411.2023 1764.9 "?" -412.2186 2214.1 "?" -416.1802 1569.1 "?" -425.2139 2586.2 "?" -427.1956 2391.1 "?" -436.2577 3485.4 "Int/PGALP/5.2ppm" -442.2464 3103.3 "a6/12.5ppm" -470.2405 9151 "b6/10.1ppm" -496.2594 3078.1 "Int/PLPGM/1.2ppm" -498.2301 3109 "?" -520.2899 2739.1 "Int/PPGAPGA-CO/4.0ppm" -526.2617 3852 "?" -539.2985 1828 "Int/PLPGMA-CO/-4.7ppm" -548.2831 5503.1 "Int/PPGAPGA/0.7ppm" -549.339 5105.4 "Int/PGALPL/-0.9ppm" -557.2015 1790.3 "?" -564.3132 2803.2 "Int/PGAPGAL/-1.5ppm" -564.4461 1473.4 "?" -567.2952 5860.9 "Int/PLPGMA/-1.3ppm" -569.3114 4720.3 "Int/PGMAIV/-0.3ppm" -571.2812 2601.4 "b7/-3.9ppm" -592.1807 1899.1 "?" -614.3491 1751.3 "?" -633.3705 7963.1 "Int/PGAPGALP-CO/-2.2ppm,Int/PPGAPGAL-CO/-2.2ppm" -640.3058 2814.4 "?" -661.3663 17369.3 "Int/PGAPGALP/-0.7ppm,Int/PPGAPGAL/-0.7ppm" -662.3647 3974.4 "Int/PGAPGALP+i/-7.5ppm,Int/PPGAPGAL+i/-7.5ppm" -680.3803 6159.2 "Int/PLPGMAI/0.5ppm" -687.8984 2815.3 "y15-NH3^2/5.9ppm" -695.8273 4004.9 "?" -699.8309 1878.5 "?" -706.7814 1733.4 "?" -711.3409 9244 "b9-H2O/-1.6ppm" -715.4171 25528.5 "y7/0.0ppm" -716.4193 6624.9 "y7+i/-0.9ppm" -720.4687 1548.7 "?" -740.657 1772 "?" -747.7864 1728.5 "?" -774.4467 2604 "Int/PGAPGALPL/-5.4ppm" -779.444 3102.9 "Int/PLPGMAIV/-5.7ppm" -792.3951 2288.2 "?" -792.5062 1866.9 "?" -793.287 2259.9 "?" -793.4606 4623.5 "y17^2/0.3ppm" -793.9547 2201.9 "y17^2+i/-9.0ppm" -843.5064 6631.8 "Int/PGAPGALPLP-CO/-2.7ppm,Int/PPGAPGALPL-CO/-2.7ppm" -871.5032 16269.2 "Int/PGAPGALPLP/-0.5ppm,Int/PPGAPGALPL/-0.5ppm" -872.5042 2808 "Int/PGAPGALPLP+i/-2.7ppm,Int/PPGAPGALPL+i/-2.7ppm" -905.4965 3245.9 "Int/PGALPLPGMA/5.7ppm" -925.5524 22654 "y9/-1.7ppm" -926.5582 6169.9 "y9+i/1.5ppm" -1025.5756 3014.9 "Int/PPGAPGALPLPG/-2.2ppm" -1038.6364 3465.3 "y10/-1.5ppm" -1050.3751 1648.4 "?" -1101.6609 1971.4 "?" -1156.626 2932.8 "Int/PPGAPGALPLPGM/6.6ppm" -1227.1982 1647 "?" -1227.6581 3903.5 "Int/PPGAPGALPLPGMA/2.2ppm" -1263.7479 15942.2 "y13/-1.1ppm" -1264.757 6224.1 "y13+i/3.8ppm" -1334.7977 1960.4 "y14/8.4ppm" -1340.7531 3560.4 "Int/PPGAPGALPLPGMAI/10.1ppm" -1356.4097 1828.1 "?" -1391.7969 3956.8 "y15/-7.9ppm" -1392.7919 2490.2 "y15+i/-13.6ppm" -1402.2483 2181.2 "?" -1466.1517 2524 "?" -1482.8165 2498.3 "?" -1488.8579 7946.7 "y16/-1.9ppm" -1489.8688 4824.6 "y16+i/3.5ppm" -1510.2008 2208.8 "?" -1511.4255 4721 "?" -1522.1158 2439.5 "?" -1554.3594 1714.9 "?" -1567.8997 3204.8 "y17-H2O/-2.0ppm" -1585.9117 37792.9 "y17/-1.1ppm" -1586.9141 23000.3 "y17+i/-1.4ppm" -1612.5677 1607.6 "?" -1616.5776 4065.9 "?" -1752.5294 2175.8 "?" -1980.9857 3567.9 "?" - -Name: AAAAGSTSVKPIFSR/2_0_44eV -MW: 1463.8086 -Comment: Single Pep=SemiTryptic Mods=0 Fullname=Q.AAAAGSTSVKPIFSR.D Charge=2 Parent=731.9043 Se=1(^G1:sc=6.33525e-018) Mz_diff=-2.7ppm HCD=44eV Scan=3052 Origfile="RO-QC-141112_Betenbaugh_HK_Fraction26.raw.FT.hcd.ch.MGF" Nreps=1/4 Sample="betenbaugh_hk4" Protein="tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1" Unassign_all=0.1681 Unassigned=0.0217 max_unassigned_ab=0.17 num_unassigned_peaks=1/20 FTResolution=15000 ms2IsolationWidth=1.90 ms1PrecursorAb=324419.29 Precursor1MaxAb=361702.23 PrecursorMonoisoMZ=731.9023 Filter="FTMS + p NSI d Full ms2 731.90@hcd34.00 [110.00-1475.00]" -Num peaks: 111 -110.1269 76.26 "?" -113.4028 68.16 "?" -115.0865 659.49 "a2/-0.8ppm" -129.1022 463.28 "IKD/-0.3ppm" -129.9147 62.91 "?" -129.9924 68.35 "?" -143.0815 2091.84 "b2/0.0ppm" -145.1529 69.39 "?" -167.7261 67.46 "?" -169.0972 508.54 "?" -175.1189 354.1 "y1/-0.3ppm,IKF/-0.3ppm,IRJ/-0.3ppm" -183.1488 80.6 "Int/PI-CO/-2.1ppm" -200.1034 223.41 "?" -214.1187 2461.15 "b3/0.4ppm" -215.1224 150.92 "b3+i/4.6ppm" -226.1194 166.15 "?" -228.0984 104.95 "?" -228.1709 81.16 "Int/VK/1.1ppm" -231.5444 76.88 "?" -240.136 109.39 "?" -242.1143 129.58 "?" -256.1299 117.54 "?" -257.1609 174.31 "a4/0.3ppm" -262.1501 113.33 "y2/-3.4ppm" -264.371 72.61 "?" -269.1243 138.11 "?" -270.1455 122.57 "?" -271.1404 453.74 "?" -281.1254 95.19 "?" -283.6823 109.92 "?" -285.1563 279.13 "b4/2.0ppm" -287.135 187.61 "?" -287.8068 65.78 "?" -297.1195 79.71 "?" -297.1555 129 "?" -299.1343 183.34 "?" -314.1814 114.14 "a5/-2.8ppm" -314.954 72.12 "?" -315.1298 108.82 "?" -342.1795 136.49 "b5/6.7ppm" -357.3935 72.21 "?" -358.2114 117.32 "Int/PIF/-3.1ppm" -370.173 101.69 "?" -374.2291 100.25 "y6^2/-0.3ppm" -384.186 84.78 "?" -390.441 73.17 "?" -392.1888 108.06 "y3-NH3/-10.3ppm" -409.2202 184.35 "y3/2.0ppm" -411.2 90.17 "b6-H2O/3.3ppm" -413.199 69.51 "?" -432.1567 69.03 "?" -457.2071 70.57 "?" -467.2223 88.32 "?" -467.28 113.01 "y8^2/1.2ppm" -469.7274 63.86 "?" -517.8033 126.12 "y9^2/0.0ppm" -522.3049 76.1 "y4/2.8ppm" -523.8322 67.7 "?" -551.1071 72.33 "?" -556.2686 106.48 "?" -561.3188 193.75 "y10^2/-0.9ppm" -561.8202 108.62 "y10^2+i/-1.0ppm" -589.8297 605.37 "y11^2/-0.6ppm" -590.3306 217.12 "y11^2+i/-1.5ppm" -602.33 179.57 "y5-NH3/0.5ppm" -613.2793 68.37 "?" -619.356 2943.26 "y5/-0.4ppm" -620.3603 685.92 "y5+i/1.9ppm" -625.349 501.99 "y12^2/0.7ppm" -625.8499 293.9 "y12^2+i/-0.2ppm" -626.1416 61.18 "?" -660.8675 419.89 "y13^2/0.5ppm" -661.3681 249.76 "y13^2+i/-0.7ppm" -667.6551 76.13 "?" -690.5546 80.2 "?" -691.2347 99.99 "?" -696.3888 148.08 "y14^2/4.4ppm" -696.8864 94.95 "y14^2+i/-1.1ppm" -699.1979 125.04 "?" -703.2349 88.5 "?" -707.3016 78.55 "?" -723.7889 71.89 "?" -730.4289 91.25 "y6-NH3/5.8ppm" -731.903 327.43 "p/-1.7ppm" -732.4063 260.03 "p+i/0.8ppm" -747.4508 1511.3 "y6/-0.5ppm" -748.4523 477.25 "y6+i/-2.3ppm" -813.9755 73.74 "?" -814.2291 68.08 "?" -846.5192 787.5 "y7/-0.5ppm" -847.5187 219.01 "y7+i/-4.5ppm" -933.5519 1204.76 "y8/0.3ppm" -934.5554 585.8 "y8+i/1.0ppm" -1034.5983 1246.92 "y9/-1.0ppm" -1035.6029 562.43 "y9+i/0.7ppm" -1043.6613 80.22 "?" -1078.0837 77.1 "?" -1121.6309 955.3 "y10/-0.4ppm" -1122.6306 445.79 "y10+i/-3.2ppm" -1160.6473 138.54 "y11-H2O/4.4ppm" -1161.6349 262.21 "y11-NH3/7.4ppm,y11-H2O+i/-8.8ppm" -1178.6521 2592.9 "y11/-0.6ppm" -1179.6555 1376.21 "y11+i/-0.1ppm" -1182.3555 67.85 "?" -1198.9932 63.25 "?" -1249.6902 1081.82 "y12/0.2ppm" -1250.691 611.72 "y12+i/-1.4ppm" -1320.7277 504.87 "y13/0.5ppm" -1321.7318 253.18 "y13+i/1.5ppm" -1389.0188 62.97 "?" -1465.9423 113.63 "?" - -Name: AAAAGSTSVKPIFSR/3_0_28eV -MW: 1464.8157 -Comment: Single Pep=SemiTryptic Mods=0 Fullname=Q.AAAAGSTSVKPIFSR.D Charge=3 Parent=488.2719 Se=1(^G1:sc=9.67069e-018) Mz_diff=3.8ppm HCD=28eV Scan=2890 Origfile="RO-QC-141112_Betenbaugh_HK_Fraction26.raw.FT.hcd.ch.MGF" Nreps=1/5 Sample="betenbaugh_hk3" Protein="tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1" Unassign_all=0.1804 Unassigned=0.0000 max_unassigned_ab=0.09 num_unassigned_peaks=0/20 FTResolution=15000 ms2IsolationWidth=1.90 ms1PrecursorAb=3390555.93 Precursor1MaxAb=3965011.86 PrecursorMonoisoMZ=488.2738 Filter="FTMS + p NSI d Full ms2 488.27@hcd34.00 [110.00-1475.00]" -Num peaks: 161 -110.4751 880.7 "?" -111.5315 809.7 "?" -112.087 1086.3 "IRG/0.7ppm" -115.0865 75818.4 "a2/-0.8ppm" -116.0703 1405.8 "IRI/-2.6ppm" -116.0899 1580.2 "a2+i/5.4ppm" -120.0808 2176.9 "IFA/0.2ppm" -129.0659 3793.3 "?" -129.1022 29530.7 "IKD/-0.3ppm" -130.1056 1054.6 "IKD+i/4.4ppm" -138.138 996.1 "?" -143.0815 89938.4 "b2/0.0ppm" -144.0849 3848.2 "b2+i/4.2ppm" -144.8468 964.9 "?" -145.0606 3718.8 "?" -153.0659 1282.7 "?" -158.0922 2201.6 "y1-NH3/-1.3ppm" -159.1125 2211.3 "?" -160.572 774.2 "?" -161.0918 1971.8 "?" -163.5364 927.8 "?" -169.0971 8412 "?" -171.0764 6416.5 "?" -175.1189 8291 "y1/-0.3ppm,IKF/-0.3ppm,IRJ/-0.3ppm" -177.5624 849.9 "?" -183.1492 2806.4 "Int/PI-CO/0.1ppm" -185.0934 958 "?" -189.0877 3809 "?" -198.0881 3160.3 "?" -200.103 8672.6 "?" -204.5067 880.9 "?" -210.0874 2471.9 "?" -211.1447 2133.4 "Int/PI/2.8ppm" -214.1187 22627.3 "b3/0.4ppm" -215.1205 976.2 "b3+i/-4.2ppm" -216.0981 4203.5 "?" -228.0981 5566.6 "y2-2NH3/1.0ppm" -228.1706 4194.9 "Int/VK/-0.2ppm" -240.0988 1395.3 "?" -240.1342 1105.3 "?" -242.1136 2814.5 "?" -244.1677 932.4 "?" -245.1246 2188.3 "y2-NH3/0.7ppm" -257.1618 1137.5 "a4/3.8ppm" -258.1086 4986.3 "?" -262.1516 3577 "y2/2.4ppm" -269.1245 3938.1 "?" -270.1448 3287.2 "?" -271.1396 2172.6 "?" -275.3359 1037 "?" -276.1198 996 "?" -276.2175 843.1 "?" -281.1246 2464.1 "?" -281.1612 873.4 "?" -285.157 1116.3 "b4/4.5ppm" -287.136 3444.7 "?" -297.1196 5420.4 "?" -299.1352 5315 "?" -310.1825 3745.4 "y5^2/2.4ppm" -315.1301 9824.1 "?" -323.1358 1153.1 "?" -333.1407 1547.3 "?" -339.168 816.3 "?" -352.1606 1609.5 "?" -357.1775 2103.4 "?" -365.7159 1399.2 "y6-NH3^2/-0.2ppm" -368.1564 3740.4 "?" -370.1726 2557.4 "?" -374.2292 5561.8 "y6^2/-0.1ppm" -374.7322 1301 "y6^2+i/4.1ppm" -376.1832 956.2 "?" -378.174 956.5 "?" -386.167 4098.3 "?" -386.2034 1795.4 "?" -392.193 3698 "y3-NH3/0.4ppm" -395.407 759.9 "?" -396.188 2827.1 "?" -404.1751 1611.3 "?" -404.2145 1149.9 "?" -409.2199 7096.2 "y3/1.2ppm" -414.1984 3857.6 "?" -420.7338 881.9 "?" -421.1867 1530.4 "?" -424.0701 904.3 "?" -439.1948 1910.9 "?" -440.9135 938 "y13^3/-0.8ppm" -457.2043 2679.7 "?" -467.2251 3238.5 "?" -467.2799 6142 "y8^2/1.0ppm" -467.7818 2674.9 "y8^2+i/1.9ppm" -485.2344 2370.1 "?" -508.7988 1318.3 "y9-H2O^2/1.6ppm" -517.804 8711.4 "y9^2/1.4ppm" -518.305 5346.7 "y9^2+i/0.5ppm" -520.2481 1151.1 "?" -522.3037 4970.1 "y4/0.5ppm" -534.7964 1651.3 "?" -538.2622 1220.7 "?" -552.317 2102.2 "y10-H2O^2/5.4ppm" -556.27 960.1 "?" -558.8151 1054.4 "?" -561.3193 9865.4 "y10^2/0.0ppm" -561.8219 3932.3 "y10^2+i/2.1ppm" -580.8237 4086.9 "y11-H2O^2/-1.8ppm" -581.3318 1582.3 "y11-H2O^2+i/9.7ppm" -589.8302 30985.9 "y11^2/0.3ppm" -590.3312 15287.5 "y11^2+i/-0.5ppm" -601.3485 2836 "y5-H2O/4.7ppm" -602.3292 3454.7 "y5-NH3/-0.8ppm" -603.3347 1573.2 "y5-NH3+i/3.5ppm" -604.2908 937.8 "?" -607.3416 3013 "?" -616.3441 2761.9 "y12-H2O^2/1.3ppm" -616.8438 2753.7 "y12-NH3^2/13.8ppm,y12-H2O^2+i/-1.5ppm" -617.736 1000.9 "?" -619.3562 112581 "y5/0.0ppm" -619.4061 1331.1 "?" -620.3597 26856.2 "y5+i/1.0ppm" -625.3489 29725.9 "y12^2/0.5ppm" -625.8499 17686.6 "y12^2+i/-0.2ppm" -651.8593 1435.9 "y13-H2O^2/-3.9ppm" -660.8666 17322.8 "y13^2/-0.8ppm" -661.3691 10845.8 "y13^2+i/0.8ppm" -665.7083 857.4 "?" -677.8406 865 "?" -679.6729 1028.1 "?" -692.6226 1839.8 "?" -696.39 1380.5 "y14^2/6.2ppm" -696.8853 1825.9 "y14^2+i/-2.6ppm" -712.8559 1575.5 "?" -729.4384 2131.4 "y6-H2O/-3.0ppm" -730.4251 3172.7 "y6-NH3/0.6ppm" -743.5792 878.1 "?" -747.4517 51670.9 "y6/0.7ppm" -748.454 16389.8 "y6+i/-0.1ppm" -846.519 23172.3 "y7/-0.7ppm" -847.5219 8878 "y7+i/-0.7ppm" -888.9458 1103 "?" -915.5491 1402.6 "y8-H2O/8.8ppm" -916.5312 1566.9 "y8-NH3/6.7ppm,y8-H2O+i/-13.9ppm" -933.5517 34961.3 "y8/0.1ppm" -934.5549 14638.2 "y8+i/0.4ppm" -962.5909 952.1 "?" -967.9422 926.5 "?" -1016.5936 1298.4 "y9-H2O/4.8ppm" -1017.5724 1109.4 "y9-NH3/-0.3ppm,y9-H2O+i/-18.9ppm" -1034.5992 17085.6 "y9/-0.1ppm" -1035.6008 7940 "y9+i/-1.3ppm" -1049.6464 924.5 "?" -1068.5891 1068.8 "?" -1072.3027 820.3 "?" -1100.4142 824.6 "?" -1121.6331 6228.7 "y10/1.6ppm" -1122.6238 3007.6 "y10+i/-9.3ppm" -1178.6527 11088.9 "y11/-0.1ppm" -1179.6552 6228.8 "y11+i/-0.4ppm" -1249.6901 2527.6 "y12/0.2ppm" -1250.6986 1715 "y12+i/4.7ppm" -1347.309 852.2 "?" -1465.9084 1527.1 "?" -1469.9915 925.5 "?" - -Name: AAAALGSHGSCSSEVEK/2_1(10,C,CAM)_50eV -MW: 1661.7668 -Comment: Single Pep=Tryptic Mods=1(10,C,CAM) Fullname=K.AAAALGSHGSCSSEVEK.E Charge=2 Parent=830.8834 Se=1(^G1:sc=6.94218e-013) Mz_diff=4.1ppm HCD=50eV Scan=1185 Origfile="RO-QC-141112_Betenbaugh_HK_Fraction18.raw.FT.hcd.ch.MGF" Nreps=1/2 Sample="betenbaugh_hk5" Protein="tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1" Unassign_all=0.4368 Unassigned=0.1840 max_unassigned_ab=0.45 num_unassigned_peaks=6/20 FTResolution=15000 ms2IsolationWidth=1.90 ms1PrecursorAb=30003.73 Precursor1MaxAb=28800.11 PrecursorMonoisoMZ=830.8868 Filter="FTMS + p NSI d Full ms2 831.38@hcd34.00 [110.00-1675.00]" -Num peaks: 68 -110.1102 57.808 "?" -115.0864 84.449 "a2/-1.6ppm" -128.1915 60.078 "?" -129.1023 157.87 "IKD/0.5ppm,y1-H2O/0.5ppm" -130.0863 143.466 "y1-NH3/0.4ppm" -134.6533 64.924 "?" -143.0814 409.786 "b2/-0.7ppm" -147.1131 319.305 "y1/2.0ppm" -151.4513 63.288 "?" -153.7949 64.094 "?" -159.3516 66.632 "?" -165.1407 62.763 "?" -185.7231 56.05 "?" -192.253 56.668 "?" -206.6181 58.523 "?" -207.8363 67.364 "?" -214.1188 604.289 "b3/0.9ppm" -240.1356 101.032 "?" -242.2549 68.729 "?" -252.7986 69.267 "?" -257.1606 92.981 "a4/-0.8ppm" -258.144 282.108 "y2-H2O/-3.2ppm" -276.1561 234.148 "y2/2.5ppm" -282.3431 71.242 "?" -285.1556 363.637 "b4/-0.5ppm" -312.7774 62.146 "?" -343.4806 65.426 "?" -355.0699 104.479 "?" -370.4347 269.799 "?" -375.2243 139.559 "y3/1.3ppm" -385.774 62.977 "?" -388.1424 58.351 "?" -431.0488 72.382 "?" -529.347 83.459 "?" -598.1849 62.213 "?" -688.806 84.319 "y13^2/-4.6ppm" -692.6966 113.075 "?" -694.6636 75.382 "?" -700.6682 128.47 "?" -725.4309 81.78 "?" -817.4878 85.857 "?" -819.1156 63.497 "?" -903.9632 63.514 "?" -982.4142 289.221 "y9/-0.4ppm" -983.42 122.064 "b11/-16.6ppm,y9+i/2.6ppm" -1036.3802 70.607 "?" -1104.5166 70.543 "?" -1119.4768 195.679 "y10/2.9ppm" -1120.4703 107.369 "y10+i/-5.3ppm" -1139.4911 84.154 "b13-H2O/1.1ppm" -1206.5106 83.121 "y11/4.2ppm" -1263.5344 229.989 "y12/5.9ppm" -1264.5262 152.204 "y12+i/-2.8ppm" -1268.5361 75.921 "b14-H2O/2.9ppm" -1286.5446 234.168 "b14/1.3ppm" -1287.5588 119.455 "b14+i/10.2ppm" -1376.6179 122.497 "y13/5.0ppm" -1376.9817 67.739 "?" -1451.4869 67.46 "?" -1465.7048 143.33 "?" -1480.5077 95.07 "?" -1522.3134 127.307 "?" -1554.5259 83.112 "?" -1595.7773 67.148 "?" -1608.2555 61.797 "?" -1623.9801 102.29 "?" -1628.4393 118.77 "?" -1670.2889 140.136 "?" - -Name: AAAALGSHGSCSSEVEK/2_1(10,C,CAM)_52eV -MW: 1661.7668 -Comment: Single Pep=Tryptic Mods=1(10,C,CAM) Fullname=K.AAAALGSHGSCSSEVEK.E Charge=2 Parent=830.8834 Se=1(^G1:sc=6.88234e-022) Mz_diff=-2.0ppm HCD=52eV Scan=868 Origfile="RO-QC-141112_Betenbaugh_HK_Fraction19.raw.FT.hcd.ch.MGF" Nreps=1/3 Sample="betenbaugh_hk2" Protein="tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1" Unassign_all=0.3390 Unassigned=0.0816 max_unassigned_ab=0.17 num_unassigned_peaks=3/20 FTResolution=15000 ms2IsolationWidth=1.90 ms1PrecursorAb=9544513.13 Precursor1MaxAb=26056925.91 PrecursorMonoisoMZ=830.8817 Filter="FTMS + p NSI d Full ms2 830.88@hcd35.00 [140.00-1675.00]" -Num peaks: 402 -141.1024 1824.4 "?" -143.0816 54472.6 "b2/0.7ppm" -144.0851 2028.2 "b2+i/5.6ppm" -147.1129 40570.6 "y1/0.7ppm" -148.1159 2104.9 "y1+i/1.9ppm" -151.6119 866.7 "?" -157.0613 1472.8 "Int/SS-H2O/3.4ppm" -157.0974 1742.9 "y1-H2O+CO/1.6ppm" -157.1335 2797.4 "?" -158.3324 771.5 "?" -158.4784 915 "?" -165.0449 784.1 "?" -169.0973 19654.9 "?" -170.1011 1507.2 "?" -170.2729 987 "?" -175.0683 1008.2 "Int/SS/-17.3ppm" -182.0172 1038.4 "?" -183.113 1337.8 "?" -183.1501 1174.6 "?" -185.1288 4333.2 "?" -195.0881 4158.9 "?" -196.1971 908.9 "?" -196.9482 1078.6 "?" -197.1034 2784.1 "?" -199.0719 3248 "?" -200.1024 1115.3 "?" -201.1237 7050.8 "?" -209.4671 931.3 "?" -211.1448 5058.2 "?" -213.1236 1676.9 "?" -213.3639 815.5 "?" -214.1189 134014 "b3/1.3ppm" -215.1223 10299.5 "b3+i/4.2ppm" -216.0974 817.8 "?" -217.0823 3500.5 "Int/SE/1.9ppm" -219.3852 836 "?" -222.1242 2551.5 "?" -225.0991 4462.1 "?" -226.1194 1819.1 "?" -229.1181 6277.7 "Int/EV/-0.8ppm,Int/VE/-0.8ppm" -234.0992 1302.3 "?" -240.1345 21406.7 "?" -240.2198 882.5 "?" -241.1192 1989.1 "y2-H2O-NH3/3.8ppm" -241.1384 1684 "?" -242.1143 4233 "?" -242.1492 2778.4 "?" -245.159 792.8 "?" -246.0991 2154.2 "?" -248.0698 1487.8 "?" -249.5848 765.4 "?" -254.1259 3540.4 "?" -256.1303 1530 "?" -256.1659 7535.6 "?" -257.1612 23103.1 "a4/1.5ppm" -258.1451 53196.9 "y2-H2O/1.0ppm" -258.1656 1886.8 "a4+i/7.9ppm" -259.1288 853.6 "y2-NH3/-0.2ppm" -259.1489 5333.4 "y2-H2O+i/4.5ppm" -264.1097 4168.1 "?" -271.1408 4874.5 "?" -276.1557 43313.6 "y2/1.1ppm" -277.1596 3627.4 "y2+i/4.7ppm" -282.1198 11960 "?" -282.1816 6243.1 "?" -285.156 70721.5 "b4/0.9ppm" -286.1596 8357.3 "b4+i/3.8ppm" -287.0818 1676.5 "?" -297.1559 2764.6 "?" -299.2081 5654.7 "?" -301.1155 1445.2 "?" -304.1141 3271.6 "?" -313.1878 2255.8 "?" -317.2701 1126.7 "?" -327.1668 2255.7 "?" -327.2031 12335.3 "?" -328.2078 1419.9 "?" -335.1022 1102.7 "?" -339.1418 3562 "?" -339.2035 4082.1 "?" -342.1779 5278.6 "?" -349.2 1115 "?" -353.2187 6849.9 "?" -355.1979 2456.3 "?" -356.2301 1374.8 "?" -358.1734 2130.2 "?" -367.2096 3137.8 "?" -369.1535 1179.9 "?" -370.2455 9499.6 "a5/1.7ppm" -371.7008 1451.4 "?" -375.2245 22737.7 "y3/1.8ppm" -376.2279 2902.4 "y3+i/3.1ppm" -377.1941 3243 "?" -382.2082 1160.7 "?" -384.2241 4525.1 "?" -387.2456 808.8 "?" -395.2044 3097.1 "?" -398.1798 1390.3 "?" -398.2402 8369.5 "b5/1.0ppm" -399.2453 1433.5 "b5+i/6.6ppm" -400.2175 1477.6 "?" -403.1794 1108.1 "?" -410.2393 1431 "?" -411.1993 2611.8 "?" -426.174 4174.1 "?" -426.2353 1747 "?" -427.2651 2092.7 "a6/-2.9ppm" -429.2092 2139.1 "?" -438.2451 2016.2 "?" -442.1512 2548.8 "?" -445.1946 994.4 "?" -446.1353 1722.5 "?" -446.1718 782.1 "?" -448.2306 1471 "?" -452.2242 2380 "?" -453.2463 1807.1 "?" -455.2633 3775.5 "b6/4.5ppm" -456.2614 1187.7 "b6+i/-5.9ppm" -464.1446 2120.7 "?" -466.2422 2050.7 "?" -471.2578 1806.9 "?" -481.1747 1118.1 "?" -481.7297 1115.4 "?" -486.2584 3180.9 "y4-H2O/5.3ppm" -490.2189 926.9 "?" -493.6116 940.7 "?" -497.2721 1445.6 "?" -499.1761 1383.7 "?" -499.2096 1262.8 "?" -504.2672 7049.8 "y4/1.6ppm" -509.2856 1991.4 "?" -511.1755 1490.7 "?" -514.2988 1812.8 "a7/0.8ppm" -523.2655 1711.6 "?" -524.2858 2612.6 "b7-H2O/5.9ppm" -528.2141 1322.9 "?" -529.1837 4266.8 "?" -533.1689 1872.9 "?" -537.2779 2429.9 "?" -539.2598 3644.5 "?" -542.2928 3010.1 "b7/-0.9ppm" -545.1652 1079 "?" -551.2365 2625.4 "y10-H2O^2/2.5ppm" -558.207 1645.1 "?" -560.241 16379.1 "y10^2/1.1ppm" -560.7422 8232.7 "y10^2+i/0.8ppm" -561.2434 3759.2 "y10^2+2i/2.4ppm" -568.1938 3165.5 "?" -572.1788 1675.8 "?" -578.2861 791.5 "?" -580.2 1614.6 "?" -582.2279 1808.4 "?" -586.2057 5627.5 "?" -588.2178 1176.6 "?" -590.1881 4182.2 "?" -591.3 7035.6 "y5/2.7ppm" -592.2983 1474.8 "y5+i/-5.2ppm" -598.2061 3432.3 "?" -603.7555 4327.2 "y11^2/-1.5ppm" -604.2574 3681.9 "y11^2+i/-0.6ppm" -604.7579 1830.1 "y11^2+2i/-0.5ppm" -608.1992 3790.4 "?" -609.7359 1059.9 "?" -614.2427 879.6 "?" -616.2162 3935 "?" -623.2614 2442.2 "y12-H2O^2/-0.7ppm" -623.7656 1586.4 "y12-NH3^2/18.8ppm,y12-H2O^2+i/3.8ppm" -632.2682 9946.8 "y12^2/1.7ppm" -632.7701 6533.9 "y12^2+i/2.5ppm" -633.2712 1699.8 "y12^2+2i/3.5ppm" -633.3458 2821.6 "?" -634.7709 1205.1 "b14-H2O^2/1.7ppm" -644.2333 1023.6 "?" -644.3076 878.1 "?" -647.3327 849.1 "?" -651.3581 8999.6 "a8/1.3ppm" -652.3618 3348.4 "a8+i/2.7ppm" -655.2262 2820.6 "?" -660.3223 1516.4 "y6-H2O/3.6ppm" -661.3433 7606.5 "b8-H2O/2.5ppm" -662.3483 1380 "b8-H2O+i/5.9ppm" -667.2252 1019.2 "?" -671.2955 1260 "y13-H2O-NH3^2/7.3ppm" -673.2364 4309.7 "?" -674.2409 1688.8 "?" -678.331 8546.4 "y6/0.8ppm" -679.2707 1080.4 "?" -679.3559 8766.1 "b8/5.4ppm" -679.8054 1687.8 "y13-H2O^2/2.2ppm" -680.3547 2791.2 "b8+i/-0.4ppm" -681.2847 1116.1 "?" -681.3271 1145.8 "?" -685.2344 1975.1 "?" -688.8099 8557.9 "y13^2/1.1ppm" -689.3101 7798.1 "y13^2+i/-0.7ppm" -689.8142 1742.5 "y13^2+2i/4.4ppm" -691.1587 1303.4 "?" -699.2916 2484.3 "?" -707.2698 3527.4 "?" -708.3794 1450.8 "a9/0.9ppm" -715.3156 1258.6 "y14-H2O^2/-9.6ppm" -717.2615 3144.1 "?" -723.9021 865.2 "?" -724.2491 3238.7 "?" -724.3282 4615.4 "y14^2/0.7ppm" -724.8292 4285.8 "y14^2+i/0.1ppm" -725.333 1740.7 "y14^2+2i/4.4ppm" -727.2462 3281.9 "?" -728.2467 1480.9 "?" -736.3738 7438.2 "b9/0.2ppm" -737.3769 2791.2 "b9+i/0.7ppm" -742.2589 5818.1 "?" -742.3272 968.1 "?" diff --git a/implementations/python/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.json b/implementations/python/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.json deleted file mode 100644 index bc6d6ba..0000000 --- a/implementations/python/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.json +++ /dev/null @@ -1,4647 +0,0 @@ -{ - "analyte_attribute_sets": { - "all": [] - }, - "attributes": [ - { - "accession": "MS:1003186", - "name": "library format version", - "value": "1.0" - }, - { - "accession": "MS:1003188", - "name": "library name", - "value": "tests/test_data/chinese_hamster_hcd_selected_head" - } - ], - "clusters": [], - "format_version": "1.0", - "interpretation_attribute_sets": { - "all": [] - }, - "spectra": [ - { - "analytes": { - "1": { - "attributes": [ - { - "accession": "MS:1000224", - "name": "molecular mass", - "value": 1710.9076 - }, - { - "accession": "MS:1000888", - "name": "stripped peptide sequence", - "value": "AAAACALTPGPLADLAAR" - }, - { - "accession": "MS:1000041", - "name": "charge state", - "value": 2 - }, - { - "accession": "MS:1001975", - "cv_param_group": "1", - "name": "delta m/z", - "value": 1.4 - }, - { - "accession": "UO:0000000", - "cv_param_group": "1", - "name": "unit", - "value": "parts per million", - "value_accession": "UO:0000169" - }, - { - "accession": "MS:1003208", - "name": "experimental precursor monoisotopic m/z", - "value": 855.455 - }, - { - "accession": "MS:1003169", - "name": "proforma peptidoform sequence", - "value": "AAAAC[Carbamidomethyl]ALTPGPLADLAAR" - }, - { - "accession": "MS:1001117", - "name": "theoretical mass", - "value": 1708.89303961159 - }, - { - "accession": "MS:1003048", - "cv_param_group": "2", - "name": "number of enzymatic termini", - "value": 2 - }, - { - "accession": "MS:1001045", - "cv_param_group": "2", - "name": "cleavage agent name", - "value": "Trypsin", - "value_accession": "MS:1001251" - }, - { - "accession": "MS:1001112", - "cv_param_group": "2", - "name": "n-terminal flanking residue", - "value": "R" - }, - { - "accession": "MS:1001113", - "cv_param_group": "2", - "name": "c-terminal flanking residue", - "value": "L" - }, - { - "accession": "MS:1000885", - "cv_param_group": "2", - "name": "protein accession", - "value": "\"tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1\"" - } - ], - "id": "1" - } - }, - "attributes": [ - { - "accession": "MS:1003237", - "name": "library spectrum key", - "value": 1 - }, - { - "accession": "MS:1003061", - 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3790.4, - 1059.9, - 879.6, - 3935.0, - 2442.2, - 1586.4, - 9946.8, - 6533.9, - 1699.8, - 2821.6, - 1205.1, - 1023.6, - 878.1, - 849.1, - 8999.6, - 3348.4, - 2820.6, - 1516.4, - 7606.5, - 1380.0, - 1019.2, - 1260.0, - 4309.7, - 1688.8, - 8546.4, - 1080.4, - 8766.1, - 1687.8, - 2791.2, - 1116.1, - 1145.8, - 1975.1, - 8557.9, - 7798.1, - 1742.5, - 1303.4, - 2484.3, - 3527.4, - 1450.8, - 1258.6, - 3144.1, - 865.2, - 3238.7, - 4615.4, - 4285.8, - 1740.7, - 3281.9, - 1480.9, - 7438.2, - 2791.2, - 5818.1, - 968.1 - ], - "interpretations": { - "1": { - "attributes": [ - { - "accession": "MS:1003079", - "name": "total unassigned intensity fraction", - "value": 0.339 - }, - { - "accession": "MS:1003080", - "name": "top 20 peak unassigned intensity fraction", - "value": 0.0816 - }, - { - "accession": "MS:1003289", - "name": "intensity of highest unassigned peak", - "value": 0.17 - }, - { - "accession": "MS:1003290", - "name": "number of unassigned peaks among top 20 peaks", - "value": 3 - } - ], - "id": "1" - } - }, - "mzs": [ - 141.1024, - 143.0816, - 144.0851, - 147.1129, - 148.1159, - 151.6119, - 157.0613, - 157.0974, - 157.1335, - 158.3324, - 158.4784, - 165.0449, - 169.0973, - 170.1011, - 170.2729, - 175.0683, - 182.0172, - 183.113, - 183.1501, - 185.1288, - 195.0881, - 196.1971, - 196.9482, - 197.1034, - 199.0719, - 200.1024, - 201.1237, - 209.4671, - 211.1448, - 213.1236, - 213.3639, - 214.1189, - 215.1223, - 216.0974, - 217.0823, - 219.3852, - 222.1242, - 225.0991, - 226.1194, - 229.1181, - 234.0992, - 240.1345, - 240.2198, - 241.1192, - 241.1384, - 242.1143, - 242.1492, - 245.159, - 246.0991, - 248.0698, - 249.5848, - 254.1259, - 256.1303, - 256.1659, - 257.1612, - 258.1451, - 258.1656, - 259.1288, - 259.1489, - 264.1097, - 271.1408, - 276.1557, - 277.1596, - 282.1198, - 282.1816, - 285.156, - 286.1596, - 287.0818, - 297.1559, - 299.2081, - 301.1155, - 304.1141, - 313.1878, - 317.2701, - 327.1668, - 327.2031, - 328.2078, - 335.1022, - 339.1418, - 339.2035, - 342.1779, - 349.2, - 353.2187, - 355.1979, - 356.2301, - 358.1734, - 367.2096, - 369.1535, - 370.2455, - 371.7008, - 375.2245, - 376.2279, - 377.1941, - 382.2082, - 384.2241, - 387.2456, - 395.2044, - 398.1798, - 398.2402, - 399.2453, - 400.2175, - 403.1794, - 410.2393, - 411.1993, - 426.174, - 426.2353, - 427.2651, - 429.2092, - 438.2451, - 442.1512, - 445.1946, - 446.1353, - 446.1718, - 448.2306, - 452.2242, - 453.2463, - 455.2633, - 456.2614, - 464.1446, - 466.2422, - 471.2578, - 481.1747, - 481.7297, - 486.2584, - 490.2189, - 493.6116, - 497.2721, - 499.1761, - 499.2096, - 504.2672, - 509.2856, - 511.1755, - 514.2988, - 523.2655, - 524.2858, - 528.2141, - 529.1837, - 533.1689, - 537.2779, - 539.2598, - 542.2928, - 545.1652, - 551.2365, - 558.207, - 560.241, - 560.7422, - 561.2434, - 568.1938, - 572.1788, - 578.2861, - 580.2, - 582.2279, - 586.2057, - 588.2178, - 590.1881, - 591.3, - 592.2983, - 598.2061, - 603.7555, - 604.2574, - 604.7579, - 608.1992, - 609.7359, - 614.2427, - 616.2162, - 623.2614, - 623.7656, - 632.2682, - 632.7701, - 633.2712, - 633.3458, - 634.7709, - 644.2333, - 644.3076, - 647.3327, - 651.3581, - 652.3618, - 655.2262, - 660.3223, - 661.3433, - 662.3483, - 667.2252, - 671.2955, - 673.2364, - 674.2409, - 678.331, - 679.2707, - 679.3559, - 679.8054, - 680.3547, - 681.2847, - 681.3271, - 685.2344, - 688.8099, - 689.3101, - 689.8142, - 691.1587, - 699.2916, - 707.2698, - 708.3794, - 715.3156, - 717.2615, - 723.9021, - 724.2491, - 724.3282, - 724.8292, - 725.333, - 727.2462, - 728.2467, - 736.3738, - 737.3769, - 742.2589, - 742.3272 - ], - "peak_annotations": [ - "?", - "b2/0.7ppm", - "b2+i/5.6ppm", - "y1/0.7ppm", - "y1+i/1.9ppm", - "?", - "m12:13-H2O/3.4ppm", - "y1-H2O+CO/1.6ppm", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "m12:13/-17.3ppm", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "b3/1.3ppm", - "b3+i/4.2ppm", - "?", - "m13:14/1.9ppm", - "?", - "?", - "?", - "?", - "m14:15/-0.8ppm,m15:16/-0.8ppm", - "?", - "?", - "?", - "y2-H2O-NH3/3.8ppm", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "a4/1.5ppm", - "y2-H2O/1.0ppm", - "a4+i/7.9ppm", - "y2-NH3/-0.2ppm", - "y2-H2O+i/4.5ppm", - "?", - "?", - "y2/1.1ppm", - "y2+i/4.7ppm", - "?", - "?", - "b4/0.9ppm", - "b4+i/3.8ppm", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "a5/1.7ppm", - "?", - "y3/1.8ppm", - "y3+i/3.1ppm", - "?", - "?", - "?", - "?", - "?", - "?", - "b5/1.0ppm", - "b5+i/6.6ppm", - "?", - "?", - "?", - "?", - "?", - "?", - "a6/-2.9ppm", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "b6/4.5ppm", - "b6+i/-5.9ppm", - "?", - "?", - "?", - "?", - "?", - "y4-H2O/5.3ppm", - "?", - "?", - "?", - "?", - "?", - "y4/1.6ppm", - "?", - "?", - "a7/0.8ppm", - "?", - "b7-H2O/5.9ppm", - "?", - "?", - "?", - "?", - "?", - "b7/-0.9ppm", - "?", - "y10-H2O^2/2.5ppm", - "?", - "y10^2/1.1ppm", - "y10+i^2/0.8ppm", - "y10+2i^2/2.4ppm", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "?", - "y5/2.7ppm", - "y5+i/-5.2ppm", - "?", - "y11^2/-1.5ppm", - "y11+i^2/-0.6ppm", - "y11+2i^2/-0.5ppm", - "?", - "?", - "?", - "?", - "y12-H2O^2/-0.7ppm", - "y12-NH3^2/18.8ppm,y12-H2O+i^2/3.8ppm", - "y12^2/1.7ppm", - "y12+i^2/2.5ppm", - "y12+2i^2/3.5ppm", - "?", - "b14-H2O^2/1.7ppm", - "?", - "?", - "?", - "a8/1.3ppm", - "a8+i/2.7ppm", - "?", - "y6-H2O/3.6ppm", - "b8-H2O/2.5ppm", - "b8-H2O+i/5.9ppm", - "?", - "y13-H2O-NH3^2/7.3ppm", - "?", - "?", - "y6/0.8ppm", - "?", - "b8/5.4ppm", - "y13-H2O^2/2.2ppm", - "b8+i/-0.4ppm", - "?", - "?", - "?", - "y13^2/1.1ppm", - "y13+i^2/-0.7ppm", - "y13+2i^2/4.4ppm", - "?", - "?", - "?", - "a9/0.9ppm", - "y14-H2O^2/-9.6ppm", - "?", - "?", - "?", - "y14^2/0.7ppm", - "y14+i^2/0.1ppm", - "y14+2i^2/4.4ppm", - "?", - "?", - "b9/0.2ppm", - "b9+i/0.7ppm", - "?", - "?" - ] - } - ], - "spectrum_attribute_sets": { - "all": [] - } -} \ No newline at end of file diff --git a/implementations/python/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.txt b/implementations/python/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.txt deleted file mode 100644 index 226cdf8..0000000 --- a/implementations/python/tests/test_data/chinese_hamster_hcd_selected_head.mzlb.txt +++ /dev/null @@ -1,1279 +0,0 @@ - -MS:1003188|library name=tests/test_data/chinese_hamster_hcd_selected_head - - - - -MS:1003061|library spectrum name=AAAACALTPGPLADLAAR/2_1(4,C,CAM)_46eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=855.4538 -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[1]MS:1000045|collision energy=46 -[1]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=5538 -MS:1003203|constituent spectrum file="CHO-K1_bRPLC_C1.RAW.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=2 -MS:1000002|sample name="jhu_cho_brplc_cam" -MS:1000028|detector resolution=7500 -[2]MS:1000828|isolation window lower offset=0.95 -[2]UO:0000000|unit=MS:1000040|m/z -[3]MS:1000829|isolation window upper offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=8799173.32 -MS:1003086|precursor apex intensity=25273307.5 -MS:1000512|filter string="FTMS + p NSI d Full ms2 855.96@hcd35.00 [140.00-1725.00]" -MS:1003059|number of peaks=87 -[4]MS:1003275|other attribute name=Se -[4]MS:1003276|other attribute value=1(^G1:sc=8.13346e-015) - -MS:1000224|molecular mass=1710.9076 -MS:1000888|stripped peptide sequence=AAAACALTPGPLADLAAR -MS:1000041|charge state=2 -[1]MS:1001975|delta m/z=1.4 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1003208|experimental precursor monoisotopic m/z=855.455 -MS:1003169|proforma peptidoform sequence=AAAAC[Carbamidomethyl]ALTPGPLADLAAR -MS:1001117|theoretical mass=1708.89303961159 -[2]MS:1003048|number of enzymatic termini=2 -[2]MS:1001045|cleavage agent name=MS:1001251|Trypsin -[2]MS:1001112|n-terminal flanking residue=R -[2]MS:1001113|c-terminal flanking residue=L -[2]MS:1000885|protein accession="tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1" - -MS:1003079|total unassigned intensity fraction=0.2848 -MS:1003080|top 20 peak unassigned intensity fraction=0.1879 -MS:1003289|intensity of highest unassigned peak=0.45 -MS:1003290|number of unassigned peaks among top 20 peaks=4 - -143.0823 14791.5 b2/5.6ppm -153.2575 5008.6 ? -159.0917 11531.8 ? -162.5977 5804.6 ? -169.0972 12931.0 ? -175.1193 18211.1 y1/2.0ppm,IR/2.0ppm -194.0699 6011.0 ? -199.1074 6737.4 ? -201.7527 5576.3 ? -212.1051 13786.1 ? -214.1195 82269.8 b3/4.1ppm -229.1552 7852.0 ? -232.0764 28555.9 ? -249.1071 4670.7 ? -257.1633 15001.9 a4/9.7ppm -276.4497 5288.0 ? -283.1411 24965.9 ? -283.3943 5090.5 ? -285.1567 48285.5 b4/3.4ppm -302.1834 10558.9 ? -303.114 52736.6 ? -317.1891 6585.3 y3/-12.9ppm -345.1593 18050.6 ? -354.1793 31400.1 b5-NH2-CO-CH2SH/5.9ppm -356.1916 7124.1 ? -370.3776 6139.7 ? -371.6662 11983.3 ? -374.1505 34930.7 ? -416.2029 8953.6 ? -417.1931 16940.5 a5/3.9ppm -425.2171 15449.8 b6-NH2-CO-CH2SH/6.6ppm -428.2024 8874.5 m5:8-H2O/14.4ppm -428.249 6831.1 ? -430.278 30118.6 y4/1.8ppm -445.1886 57883.2 b5/5.0ppm -446.2049 8868.2 m5:8/-4.2ppm -457.1753 5403.5 ? -467.2682 6117.4 ? -469.2735 6906.4 ? -471.2018 9435.3 ? -487.2299 15480.3 ? -488.2367 13813.7 a6/16.6ppm -490.7795 12739.9 y10^2/-0.6ppm -491.2839 6651.0 y10+i^2/5.4ppm -495.9153 6370.5 ? -499.2364 5273.9 m4:8-H2O/6.2ppm -516.2236 49862.4 b6/0.2ppm -528.2323 9881.3 ? -530.2752 10333.1 ? -541.3164 7041.3 ? -545.308 6833.8 y5/7.0ppm -558.2726 23958.7 ? -570.3232 6006.3 ? -601.3148 11919.6 a7/3.6ppm -617.2834 5841.2 ? -617.3372 4342.1 ? -629.3052 22419.3 b7/-3.7ppm -641.3058 11147.2 m2:8-H2O/-2.7ppm -659.3259 9164.2 m2:8/11.8ppm -685.3383 6861.0 ? -712.3472 13798.2 b8-H2O/3.6ppm -730.3578 16426.3 b8/3.5ppm -826.4765 18892.5 y8/-2.0ppm -855.017 7062.7 ? -855.5167 249849.0 ? -856.523 57946.3 ? -883.4993 29383.7 y9/-0.3ppm -922.4447 6413.2 ? -934.4906 6605.4 ? -963.5431 13545.1 y10-NH3/17.9ppm -980.556 559065.0 y10/3.7ppm -981.5587 216762.0 y10+i/3.6ppm -1037.5859 14218.2 ? -1038.5812 9574.2 ? -1067.8983 6611.6 ? -1081.6041 179858.0 y11/3.8ppm -1082.6077 79540.9 y11+i/4.5ppm -1143.0283 6099.8 ? -1194.6899 106907.0 y12/4.9ppm -1195.6869 50339.1 y12+i/-0.1ppm -1265.7273 83029.7 y13/4.8ppm -1266.7281 42164.7 y13+i/3.2ppm -1390.1328 5531.5 ? -1395.6904 8549.2 ? -1425.7538 51400.1 y14/1.4ppm -1426.7601 40643.8 y14+i/3.8ppm -1496.7792 11918.3 y15/-6.5ppm - - -MS:1003061|library spectrum name=AAAACALTPGPLADLAAR/2_1(4,C,CAM)_53eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=855.4538 -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[1]MS:1000045|collision energy=53 -[1]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=6275 -MS:1003203|constituent spectrum file="RO-QC-141112_Betenbaugh_HK_Fraction46.raw.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=14 -MS:1000002|sample name="betenbaugh_hk2" -MS:1000028|detector resolution=15000 -[2]MS:1000828|isolation window lower offset=0.95 -[2]UO:0000000|unit=MS:1000040|m/z -[3]MS:1000829|isolation window upper offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=1776618.56 -MS:1003086|precursor apex intensity=12167259.65 -MS:1000512|filter string="FTMS + p NSI d Full ms2 855.95@hcd35.00 [140.00-1725.00]" -MS:1003059|number of peaks=204 -[4]MS:1003275|other attribute name=Se -[4]MS:1003276|other attribute value=1(^G1:sc=1.31932e-020) - -MS:1000224|molecular mass=1710.9076 -MS:1000888|stripped peptide sequence=AAAACALTPGPLADLAAR -MS:1000041|charge state=2 -[1]MS:1001975|delta m/z=4.2 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1003208|experimental precursor monoisotopic m/z=855.4574 -MS:1003169|proforma peptidoform sequence=AAAAC[Carbamidomethyl]ALTPGPLADLAAR -MS:1001117|theoretical mass=1708.89303961159 -[2]MS:1003048|number of enzymatic termini=2 -[2]MS:1001045|cleavage agent name=MS:1001251|Trypsin -[2]MS:1001112|n-terminal flanking residue=R -[2]MS:1001113|c-terminal flanking residue=L -[2]MS:1000885|protein accession="tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1" - -MS:1003079|total unassigned intensity fraction=0.3165 -MS:1003080|top 20 peak unassigned intensity fraction=0.142 -MS:1003289|intensity of highest unassigned peak=0.16 -MS:1003290|number of unassigned peaks among top 20 peaks=5 - -143.0814 9555.6 b2/-0.7ppm -169.097 5174.5 ? -171.1126 2428.2 ? -175.1069 1175.7 ? -175.1187 7806.9 y1/-1.4ppm,IR/-1.4ppm -178.0645 645.1 ? -181.0971 2623.7 ? -183.1495 1770.8 m11:12-CO/1.7ppm -185.0921 4004.0 ? -185.1288 983.4 m12:13/1.9ppm -199.1073 2854.3 ? -203.1022 2225.3 ? -203.412 489.7 ? -204.0803 4532.0 ? -211.1438 1671.5 m11:12/-1.4ppm -212.103 6959.1 y2-2NH3/0.2ppm -214.1185 23984.8 b3/-0.5ppm -215.0481 1035.3 ? -215.1219 1943.5 b3+i/2.3ppm -215.1392 1652.7 m7:8/0.8ppm -216.0967 632.6 ? -229.1299 970.3 y2-NH3/1.7ppm -231.1446 601.8 ? -232.0748 11826.6 ? -235.1929 547.3 ? -240.1344 3195.6 ? -242.1137 1025.5 ? -246.1558 1514.8 y2/-1.1ppm -255.1454 790.9 ? -256.1652 1376.9 ? -257.1605 3523.6 a4/-1.2ppm -258.0901 1119.1 ? -268.1656 1623.7 m6:8-H2O/0.1ppm -282.1807 1542.2 m11:13/-1.8ppm -283.14 10639.1 ? -284.1443 1021.0 ? -285.1555 11955.3 b4/-0.8ppm -286.1599 1072.8 b4+i/4.8ppm -286.1761 2533.2 m6:8/-0.1ppm -293.366 528.7 ? -298.177 1429.9 ? -302.1818 2634.5 ? -303.1121 15782.5 ? -304.1151 1344.9 ? -309.1558 945.0 ? -311.1712 2335.2 ? -317.1934 2115.0 y3/0.7ppm -327.2036 961.2 ? -328.1647 1131.6 ? -329.1273 3077.6 ? -331.1088 859.4 ? -337.2232 2252.0 m9:12-CO/-0.6ppm -339.2033 1220.8 ? -341.1834 794.7 ? -345.1589 6582.2 ? -346.1541 1361.2 ? -353.2189 1800.0 ? -354.1769 9317.5 b5-NH2-CO-CH2SH/-0.8ppm -355.1793 1293.7 b5-NH2-CO-CH2SH+i/-1.9ppm -356.1933 1800.3 ? -357.211 686.5 ? -358.2065 618.4 ? -363.3883 563.8 ? -365.2181 2776.2 y7^2/4.9ppm -366.2212 705.5 ? -368.1942 682.0 ? -369.3904 685.6 ? -370.4914 4171.5 ? -372.1714 835.1 ? -374.149 10475.6 ? -375.153 1112.5 ? -380.1929 960.8 ? -384.1859 584.6 ? -386.2027 978.1 ? -396.2243 975.1 ? -397.2071 1560.8 m11:14/-2.7ppm -398.2401 1130.2 ? -400.1644 4875.2 ? -401.1676 730.6 ? -402.1434 1170.3 ? -408.2588 885.8 m9:13-CO/-4.2ppm -410.2415 678.5 ? -416.1944 2264.1 ? -417.192 3203.6 a5/1.3ppm -418.1938 714.5 a5+i/-0.6ppm -422.2396 762.6 ? -425.2144 2490.8 b6-NH2-CO-CH2SH/0.2ppm -428.1953 1647.7 m5:8-H2O/-2.1ppm -430.2767 20600.0 y4/-1.3ppm -431.2812 3236.0 y4+i/2.9ppm -436.2548 3128.6 m9:13/-1.5ppm -442.2117 1223.9 ? -445.1862 10843.9 b5/-0.4ppm -446.1865 1519.0 b5+i/-5.6ppm -446.2101 1269.8 m5:8/7.4ppm -454.23 854.8 ? -459.2378 1549.6 ? -471.2021 2150.3 ? -473.1871 733.9 ? -474.2351 776.1 ? -487.2318 3002.2 ? -488.2279 2861.1 a6/-1.4ppm -490.7802 1998.5 y10^2/0.8ppm -493.2748 802.6 ? -499.2884 798.8 ? -505.2755 1577.1 ? -513.2489 2142.4 ? -516.223 7108.2 b6/-1.0ppm -517.22 1175.7 b6+i/-11.9ppm -528.2206 1033.3 ? -528.2757 1044.1 y5-NH3/-3.7ppm -530.2791 1202.4 ? -533.272 1261.5 ? -535.1867 572.4 ? -543.2589 744.4 ? -545.3041 3290.4 y5/-0.2ppm -546.2418 626.0 ? -546.3103 815.6 y5+i/6.2ppm -551.2829 4018.4 m9:14/0.9ppm -552.287 815.2 m9:14+i/3.0ppm -558.2695 4055.3 ? -559.2736 821.5 ? -570.2687 978.2 m3:8-H2O/-3.1ppm -588.277 1266.6 m3:8/-6.8ppm -601.3116 1037.7 a7/-1.7ppm -609.3334 1558.5 ? -616.3435 2514.4 y6/3.6ppm -629.3079 1030.1 b7/0.5ppm -636.3726 1099.2 m9:15-CO/1.7ppm -638.3498 623.7 ? -641.3058 1372.7 m2:8-H2O/-2.7ppm -659.3138 896.8 m2:8/-6.6ppm -664.3644 2215.2 m9:15/-3.1ppm -665.3702 616.9 m9:15+i/1.2ppm -698.652 964.9 ? -710.8712 676.6 ? -712.343 766.7 b8-H2O/-2.3ppm -728.644 669.7 ? -729.4229 1339.5 y7/-3.4ppm -730.3568 859.0 b8/2.1ppm -735.4047 1839.2 m9:16/1.5ppm -735.7518 597.0 ? -736.4097 726.4 b9-NH2-CO-CH2SH/14.8ppm,m9:16+i/4.3ppm -758.5785 584.4 ? -804.5634 599.5 ? -806.4404 871.1 m9:17/-0.3ppm -807.4396 706.8 m9:17+i/-5.0ppm -809.4468 1047.0 y8-NH3/-5.9ppm -826.4767 5889.7 y8/-1.7ppm -827.4818 1704.1 y8+i/1.0ppm -835.4305 6503.5 ? -836.4305 855.7 ? -855.5272 1972.3 ? -883.499 11027.3 y9/-0.7ppm -884.5011 4136.3 y9+i/-1.5ppm -920.521 899.9 ? -922.4631 6661.9 ? -923.4683 1004.4 ? -938.5323 694.4 ? -954.0876 657.8 ? -962.5461 1056.8 y10-H2O/4.5ppm -963.5266 5559.2 y10-NH3/0.8ppm -964.5276 3037.9 y10-NH3+i/-1.1ppm -980.5516 101168.0 y10/-0.8ppm -981.5547 48825.1 y10+i/-0.5ppm -982.556 3169.3 y10+2i/-1.8ppm -998.153 653.4 ? -1026.4183 641.1 ? -1033.4918 1042.9 ? -1037.5729 7440.8 ? -1038.5754 4253.3 ? -1050.5208 5312.6 ? -1063.5883 1995.7 y11-H2O/-1.1ppm -1064.5804 1437.3 y11-NH3/6.5ppm,y11-H2O+i/-11.2ppm -1081.5985 28537.7 y11/-1.4ppm -1082.6017 16194.1 y11+i/-1.1ppm -1083.5983 1228.4 y11+2i/-6.6ppm -1150.6531 1305.7 ? -1176.6824 1518.9 y12-H2O/7.5ppm -1177.6671 1170.1 y12-NH3/8.1ppm,y12-H2O+i/-7.9ppm -1182.254 639.1 ? -1194.6826 20850.2 y12/-1.3ppm -1195.6853 12324.9 y12+i/-1.4ppm -1197.5858 4604.9 ? -1221.6934 1065.9 ? -1247.7007 1013.5 y13-H2O/-8.0ppm -1252.6328 702.9 ? -1265.7198 16380.4 y13/-1.1ppm -1266.7246 9779.2 y13+i/0.4ppm -1267.7239 747.9 y13+2i/-2.2ppm -1298.6331 3899.6 ? -1334.7629 576.6 y14-NH2-CO-CH2SH/15.2ppm -1395.6888 9418.6 ? -1396.6947 2451.5 ? -1407.7356 1083.1 y14-H2O/-4.0ppm -1408.7473 1011.7 y14-NH3/15.6ppm,y14-H2O+i/2.3ppm -1425.7515 7609.8 y14/-0.3ppm -1426.7562 7554.0 y14+i/1.1ppm -1466.0739 798.5 ? -1495.1215 635.8 ? -1496.7932 1534.6 y15/2.8ppm -1497.7944 1455.0 y15+i/1.7ppm -1557.3423 600.8 ? -1628.3004 719.6 ? - - -MS:1003061|library spectrum name=AAAAGQTGTVPPGAPGALPLPGMAIVK/2_0_76eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=1207.1672 -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[1]MS:1000045|collision energy=76 -[1]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=7528 -MS:1003203|constituent spectrum file="RO-QC-141112_Betenbaugh_HK_Fraction18.raw.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=2 -MS:1000002|sample name="betenbaugh_hk1" -MS:1000028|detector resolution=15000 -[2]MS:1000828|isolation window lower offset=0.95 -[2]UO:0000000|unit=MS:1000040|m/z -[3]MS:1000829|isolation window upper offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=6939079.2 -MS:1003086|precursor apex intensity=7583304.35 -MS:1000512|filter string="FTMS + p NSI d Full ms2 1207.67@hcd35.00 [140.00-2000.00]" -MS:1003059|number of peaks=122 -[4]MS:1003275|other attribute name=Se -[4]MS:1003276|other attribute value=1(^G1:sc=1.43642e-012) - -MS:1000224|molecular mass=2414.3344 -MS:1000888|stripped peptide sequence=AAAAGQTGTVPPGAPGALPLPGMAIVK -MS:1000041|charge state=2 -[1]MS:1001975|delta m/z=-0.9 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1003208|experimental precursor monoisotopic m/z=1207.1661 -MS:1003169|proforma peptidoform sequence=AAAAGQTGTVPPGAPGALPLPGMAIVK -MS:1001117|theoretical mass=2412.319901150229 -[2]MS:1003048|number of enzymatic termini=1 -[2]MS:1001045|cleavage agent name=MS:1001251|Trypsin -[2]MS:1001112|n-terminal flanking residue=A -[2]MS:1001113|c-terminal flanking residue=E -[2]MS:1000885|protein accession="tr|G3I2Q7|G3I2Q7_CRIGR Transcription intermediary factor 1-beta OS=Cricetulus griseus GN=I79_017700 PE=4 SV=1" - -MS:1003079|total unassigned intensity fraction=0.2591 -MS:1003080|top 20 peak unassigned intensity fraction=0.0 -MS:1003289|intensity of highest unassigned peak=0.12 -MS:1003290|number of unassigned peaks among top 20 peaks=0 - -143.0816 2935.3 b2/0.7ppm -147.1127 2210.5 y1/-0.7ppm -154.4137 1587.1 ? -155.0816 2825.2 m12:13/0.6ppm -169.771 1665.2 ? -176.5942 1535.3 ? -181.0984 2034.3 ? -186.0873 2509.4 ? -198.5815 1458.2 ? -199.2009 1692.3 ? -206.924 1799.6 ? -214.1185 6874.5 b3/-0.5ppm -214.6242 1695.0 ? -216.197 1659.5 ? -224.6321 1496.3 ? -226.1183 6292.8 m12:14/-1.4ppm -227.4689 1609.1 ? -230.1134 2157.9 ? -240.1377 1613.7 ? -246.1817 2500.8 y2/2.0ppm -252.1353 2976.9 m11:13/4.1ppm -257.1249 2901.5 ? -257.1618 2468.8 a4/3.8ppm -266.3697 1813.9 ? -283.6819 1747.3 ? -285.1557 5707.9 b4/-0.1ppm -285.8154 1730.9 ? -287.1343 2200.9 ? -295.139 1768.2 ? -295.1769 3116.9 m12:15-CO/1.5ppm,m11:14-CO/1.5ppm -323.1715 9768.4 m12:15/0.4ppm,m11:14/0.4ppm -326.1471 1541.0 ? -328.1606 3372.4 ? -339.2022 4142.5 m15:18/-1.4ppm -342.1785 2123.8 b5/3.8ppm -357.1593 8559.3 m21:24/0.6ppm -368.2019 1424.3 ? -370.1709 2286.1 ? -382.171 2478.3 ? -399.199 2560.8 ? -404.719 1744.2 ? -411.2023 1764.9 ? -412.2186 2214.1 ? -416.1802 1569.1 ? -425.2139 2586.2 ? -427.1956 2391.1 ? -436.2577 3485.4 m15:19/5.2ppm -442.2464 3103.3 a6/12.5ppm -470.2405 9151.0 b6/10.1ppm -496.2594 3078.1 m19:23/1.2ppm -498.2301 3109.0 ? -520.2899 2739.1 m11:17-CO/4.0ppm -526.2617 3852.0 ? -539.2985 1828.0 m19:24-CO/-4.7ppm -548.2831 5503.1 m11:17/0.7ppm -549.339 5105.4 m15:20/-0.9ppm -557.2015 1790.3 ? -564.3132 2803.2 m12:18/-1.5ppm -564.4461 1473.4 ? -567.2952 5860.9 m19:24/-1.3ppm -569.3114 4720.3 m21:26/-0.3ppm -571.2812 2601.4 b7/-3.9ppm -592.1807 1899.1 ? -614.3491 1751.3 ? -633.3705 7963.1 m12:19-CO/-2.2ppm,m11:18-CO/-2.2ppm -640.3058 2814.4 ? -661.3663 17369.3 m12:19/-0.7ppm,m11:18/-0.7ppm -662.3647 3974.4 m12:19+i/-7.5ppm,m11:18+i/-7.5ppm -680.3803 6159.2 m19:25/0.5ppm -687.8984 2815.3 y15-NH3^2/5.9ppm -695.8273 4004.9 ? -699.8309 1878.5 ? -706.7814 1733.4 ? -711.3409 9244.0 b9-H2O/-1.6ppm -715.4171 25528.5 y7/0.0ppm -716.4193 6624.9 y7+i/-0.9ppm -720.4687 1548.7 ? -740.657 1772.0 ? -747.7864 1728.5 ? -774.4467 2604.0 m12:20/-5.4ppm -779.444 3102.9 m19:26/-5.7ppm -792.3951 2288.2 ? -792.5062 1866.9 ? -793.287 2259.9 ? -793.4606 4623.5 y17^2/0.3ppm -793.9547 2201.9 y17+i^2/-9.0ppm -843.5064 6631.8 m12:21-CO/-2.7ppm,m11:20-CO/-2.7ppm -871.5032 16269.2 m12:21/-0.5ppm,m11:20/-0.5ppm -872.5042 2808.0 m12:21+i/-2.7ppm,m11:20+i/-2.7ppm -905.4965 3245.9 m15:24/5.7ppm -925.5524 22654.0 y9/-1.7ppm -926.5582 6169.9 y9+i/1.5ppm -1025.5756 3014.9 m11:22/-2.2ppm -1038.6364 3465.3 y10/-1.5ppm -1050.3751 1648.4 ? -1101.6609 1971.4 ? -1156.626 2932.8 m11:23/6.6ppm -1227.1982 1647.0 ? -1227.6581 3903.5 m11:24/2.2ppm -1263.7479 15942.2 y13/-1.1ppm -1264.757 6224.1 y13+i/3.8ppm -1334.7977 1960.4 y14/8.4ppm -1340.7531 3560.4 m11:25/10.1ppm -1356.4097 1828.1 ? -1391.7969 3956.8 y15/-7.9ppm -1392.7919 2490.2 y15+i/-13.6ppm -1402.2483 2181.2 ? -1466.1517 2524.0 ? -1482.8165 2498.3 ? -1488.8579 7946.7 y16/-1.9ppm -1489.8688 4824.6 y16+i/3.5ppm -1510.2008 2208.8 ? -1511.4255 4721.0 ? -1522.1158 2439.5 ? -1554.3594 1714.9 ? -1567.8997 3204.8 y17-H2O/-2.0ppm -1585.9117 37792.9 y17/-1.1ppm -1586.9141 23000.3 y17+i/-1.4ppm -1612.5677 1607.6 ? -1616.5776 4065.9 ? -1752.5294 2175.8 ? -1980.9857 3567.9 ? - - -MS:1003061|library spectrum name=AAAAGSTSVKPIFSR/2_0_44eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=731.9043 -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[1]MS:1000045|collision energy=44 -[1]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=3052 -MS:1003203|constituent spectrum file="RO-QC-141112_Betenbaugh_HK_Fraction26.raw.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=4 -MS:1000002|sample name="betenbaugh_hk4" -MS:1000028|detector resolution=15000 -[2]MS:1000828|isolation window lower offset=0.95 -[2]UO:0000000|unit=MS:1000040|m/z -[3]MS:1000829|isolation window upper offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=324419.29 -MS:1003086|precursor apex intensity=361702.23 -MS:1000512|filter string="FTMS + p NSI d Full ms2 731.90@hcd34.00 [110.00-1475.00]" -MS:1003059|number of peaks=111 -[4]MS:1003275|other attribute name=Se -[4]MS:1003276|other attribute value=1(^G1:sc=6.33525e-018) - -MS:1000224|molecular mass=1463.8086 -MS:1000888|stripped peptide sequence=AAAAGSTSVKPIFSR -MS:1000041|charge state=2 -[1]MS:1001975|delta m/z=-2.7 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1003208|experimental precursor monoisotopic m/z=731.9023 -MS:1003169|proforma peptidoform sequence=AAAAGSTSVKPIFSR -MS:1001117|theoretical mass=1461.7939769138902 -[2]MS:1003048|number of enzymatic termini=1 -[2]MS:1001045|cleavage agent name=MS:1001251|Trypsin -[2]MS:1001112|n-terminal flanking residue=Q -[2]MS:1001113|c-terminal flanking residue=D -[2]MS:1000885|protein accession="tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1" - -MS:1003079|total unassigned intensity fraction=0.1681 -MS:1003080|top 20 peak unassigned intensity fraction=0.0217 -MS:1003289|intensity of highest unassigned peak=0.17 -MS:1003290|number of unassigned peaks among top 20 peaks=1 - -110.1269 76.26 ? -113.4028 68.16 ? -115.0865 659.49 a2/-0.8ppm -129.1022 463.28 IK/-0.3ppm -129.9147 62.91 ? -129.9924 68.35 ? -143.0815 2091.84 b2/0.0ppm -145.1529 69.39 ? -167.7261 67.46 ? -169.0972 508.54 ? -175.1189 354.1 y1/-0.3ppm,IK/-0.3ppm,IR/-0.3ppm -183.1488 80.6 m11:12-CO/-2.1ppm -200.1034 223.41 ? -214.1187 2461.15 b3/0.4ppm -215.1224 150.92 b3+i/4.6ppm -226.1194 166.15 ? -228.0984 104.95 ? -228.1709 81.16 m9:10/1.1ppm -231.5444 76.88 ? -240.136 109.39 ? -242.1143 129.58 ? -256.1299 117.54 ? -257.1609 174.31 a4/0.3ppm -262.1501 113.33 y2/-3.4ppm -264.371 72.61 ? -269.1243 138.11 ? -270.1455 122.57 ? -271.1404 453.74 ? -281.1254 95.19 ? -283.6823 109.92 ? -285.1563 279.13 b4/2.0ppm -287.135 187.61 ? -287.8068 65.78 ? -297.1195 79.71 ? -297.1555 129.0 ? -299.1343 183.34 ? -314.1814 114.14 a5/-2.8ppm -314.954 72.12 ? -315.1298 108.82 ? -342.1795 136.49 b5/6.7ppm -357.3935 72.21 ? -358.2114 117.32 m11:13/-3.1ppm -370.173 101.69 ? -374.2291 100.25 y6^2/-0.3ppm -384.186 84.78 ? -390.441 73.17 ? -392.1888 108.06 y3-NH3/-10.3ppm -409.2202 184.35 y3/2.0ppm -411.2 90.17 b6-H2O/3.3ppm -413.199 69.51 ? -432.1567 69.03 ? -457.2071 70.57 ? -467.2223 88.32 ? -467.28 113.01 y8^2/1.2ppm -469.7274 63.86 ? -517.8033 126.12 y9^2/0.0ppm -522.3049 76.1 y4/2.8ppm -523.8322 67.7 ? -551.1071 72.33 ? -556.2686 106.48 ? -561.3188 193.75 y10^2/-0.9ppm -561.8202 108.62 y10+i^2/-1.0ppm -589.8297 605.37 y11^2/-0.6ppm -590.3306 217.12 y11+i^2/-1.5ppm -602.33 179.57 y5-NH3/0.5ppm -613.2793 68.37 ? -619.356 2943.26 y5/-0.4ppm -620.3603 685.92 y5+i/1.9ppm -625.349 501.99 y12^2/0.7ppm -625.8499 293.9 y12+i^2/-0.2ppm -626.1416 61.18 ? -660.8675 419.89 y13^2/0.5ppm -661.3681 249.76 y13+i^2/-0.7ppm -667.6551 76.13 ? -690.5546 80.2 ? -691.2347 99.99 ? -696.3888 148.08 y14^2/4.4ppm -696.8864 94.95 y14+i^2/-1.1ppm -699.1979 125.04 ? -703.2349 88.5 ? -707.3016 78.55 ? -723.7889 71.89 ? -730.4289 91.25 y6-NH3/5.8ppm -731.903 327.43 p/-1.7ppm -732.4063 260.03 p+i/0.8ppm -747.4508 1511.3 y6/-0.5ppm -748.4523 477.25 y6+i/-2.3ppm -813.9755 73.74 ? -814.2291 68.08 ? -846.5192 787.5 y7/-0.5ppm -847.5187 219.01 y7+i/-4.5ppm -933.5519 1204.76 y8/0.3ppm -934.5554 585.8 y8+i/1.0ppm -1034.5983 1246.92 y9/-1.0ppm -1035.6029 562.43 y9+i/0.7ppm -1043.6613 80.22 ? -1078.0837 77.1 ? -1121.6309 955.3 y10/-0.4ppm -1122.6306 445.79 y10+i/-3.2ppm -1160.6473 138.54 y11-H2O/4.4ppm -1161.6349 262.21 y11-NH3/7.4ppm,y11-H2O+i/-8.8ppm -1178.6521 2592.9 y11/-0.6ppm -1179.6555 1376.21 y11+i/-0.1ppm -1182.3555 67.85 ? -1198.9932 63.25 ? -1249.6902 1081.82 y12/0.2ppm -1250.691 611.72 y12+i/-1.4ppm -1320.7277 504.87 y13/0.5ppm -1321.7318 253.18 y13+i/1.5ppm -1389.0188 62.97 ? -1465.9423 113.63 ? - - -MS:1003061|library spectrum name=AAAAGSTSVKPIFSR/3_0_28eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=488.2719 -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[1]MS:1000045|collision energy=28 -[1]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=2890 -MS:1003203|constituent spectrum file="RO-QC-141112_Betenbaugh_HK_Fraction26.raw.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=5 -MS:1000002|sample name="betenbaugh_hk3" -MS:1000028|detector resolution=15000 -[2]MS:1000828|isolation window lower offset=0.95 -[2]UO:0000000|unit=MS:1000040|m/z -[3]MS:1000829|isolation window upper offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=3390555.93 -MS:1003086|precursor apex intensity=3965011.86 -MS:1000512|filter string="FTMS + p NSI d Full ms2 488.27@hcd34.00 [110.00-1475.00]" -MS:1003059|number of peaks=161 -[4]MS:1003275|other attribute name=Se -[4]MS:1003276|other attribute value=1(^G1:sc=9.67069e-018) - -MS:1000224|molecular mass=1464.8157 -MS:1000888|stripped peptide sequence=AAAAGSTSVKPIFSR -MS:1000041|charge state=3 -[1]MS:1001975|delta m/z=3.8 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1003208|experimental precursor monoisotopic m/z=488.2738 -MS:1003169|proforma peptidoform sequence=AAAAGSTSVKPIFSR -MS:1001117|theoretical mass=1461.7939769138902 -[2]MS:1003048|number of enzymatic termini=1 -[2]MS:1001045|cleavage agent name=MS:1001251|Trypsin -[2]MS:1001112|n-terminal flanking residue=Q -[2]MS:1001113|c-terminal flanking residue=D -[2]MS:1000885|protein accession="tr|G3I0F4|G3I0F4_CRIGR NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 OS=Cricetulus griseus GN=I79_016836 PE=4 SV=1" - -MS:1003079|total unassigned intensity fraction=0.1804 -MS:1003080|top 20 peak unassigned intensity fraction=0.0 -MS:1003289|intensity of highest unassigned peak=0.09 -MS:1003290|number of unassigned peaks among top 20 peaks=0 - -110.4751 880.7 ? -111.5315 809.7 ? -112.087 1086.3 IR/0.7ppm -115.0865 75818.4 a2/-0.8ppm -116.0703 1405.8 IR/-2.6ppm -116.0899 1580.2 a2+i/5.4ppm -120.0808 2176.9 IF/0.2ppm -129.0659 3793.3 ? -129.1022 29530.7 IK/-0.3ppm -130.1056 1054.6 IK+i/4.4ppm -138.138 996.1 ? -143.0815 89938.4 b2/0.0ppm -144.0849 3848.2 b2+i/4.2ppm -144.8468 964.9 ? -145.0606 3718.8 ? -153.0659 1282.7 ? -158.0922 2201.6 y1-NH3/-1.3ppm -159.1125 2211.3 ? -160.572 774.2 ? -161.0918 1971.8 ? -163.5364 927.8 ? -169.0971 8412.0 ? -171.0764 6416.5 ? -175.1189 8291.0 y1/-0.3ppm,IK/-0.3ppm,IR/-0.3ppm -177.5624 849.9 ? -183.1492 2806.4 m11:12-CO/0.1ppm -185.0934 958.0 ? -189.0877 3809.0 ? -198.0881 3160.3 ? -200.103 8672.6 ? -204.5067 880.9 ? -210.0874 2471.9 ? -211.1447 2133.4 m11:12/2.8ppm -214.1187 22627.3 b3/0.4ppm -215.1205 976.2 b3+i/-4.2ppm -216.0981 4203.5 ? -228.0981 5566.6 y2-2NH3/1.0ppm -228.1706 4194.9 m9:10/-0.2ppm -240.0988 1395.3 ? -240.1342 1105.3 ? -242.1136 2814.5 ? -244.1677 932.4 ? -245.1246 2188.3 y2-NH3/0.7ppm -257.1618 1137.5 a4/3.8ppm -258.1086 4986.3 ? -262.1516 3577.0 y2/2.4ppm -269.1245 3938.1 ? -270.1448 3287.2 ? -271.1396 2172.6 ? -275.3359 1037.0 ? -276.1198 996.0 ? -276.2175 843.1 ? -281.1246 2464.1 ? -281.1612 873.4 ? -285.157 1116.3 b4/4.5ppm -287.136 3444.7 ? -297.1196 5420.4 ? -299.1352 5315.0 ? -310.1825 3745.4 y5^2/2.4ppm -315.1301 9824.1 ? -323.1358 1153.1 ? -333.1407 1547.3 ? -339.168 816.3 ? -352.1606 1609.5 ? -357.1775 2103.4 ? -365.7159 1399.2 y6-NH3^2/-0.2ppm -368.1564 3740.4 ? -370.1726 2557.4 ? -374.2292 5561.8 y6^2/-0.1ppm -374.7322 1301.0 y6+i^2/4.1ppm -376.1832 956.2 ? -378.174 956.5 ? -386.167 4098.3 ? -386.2034 1795.4 ? -392.193 3698.0 y3-NH3/0.4ppm -395.407 759.9 ? -396.188 2827.1 ? -404.1751 1611.3 ? -404.2145 1149.9 ? -409.2199 7096.2 y3/1.2ppm -414.1984 3857.6 ? -420.7338 881.9 ? -421.1867 1530.4 ? -424.0701 904.3 ? -439.1948 1910.9 ? -440.9135 938.0 y13^3/-0.8ppm -457.2043 2679.7 ? -467.2251 3238.5 ? -467.2799 6142.0 y8^2/1.0ppm -467.7818 2674.9 y8+i^2/1.9ppm -485.2344 2370.1 ? -508.7988 1318.3 y9-H2O^2/1.6ppm -517.804 8711.4 y9^2/1.4ppm -518.305 5346.7 y9+i^2/0.5ppm -520.2481 1151.1 ? -522.3037 4970.1 y4/0.5ppm -534.7964 1651.3 ? -538.2622 1220.7 ? -552.317 2102.2 y10-H2O^2/5.4ppm -556.27 960.1 ? -558.8151 1054.4 ? -561.3193 9865.4 y10^2/0.0ppm -561.8219 3932.3 y10+i^2/2.1ppm -580.8237 4086.9 y11-H2O^2/-1.8ppm -581.3318 1582.3 y11-H2O+i^2/9.7ppm -589.8302 30985.9 y11^2/0.3ppm -590.3312 15287.5 y11+i^2/-0.5ppm -601.3485 2836.0 y5-H2O/4.7ppm -602.3292 3454.7 y5-NH3/-0.8ppm -603.3347 1573.2 y5-NH3+i/3.5ppm -604.2908 937.8 ? -607.3416 3013.0 ? -616.3441 2761.9 y12-H2O^2/1.3ppm -616.8438 2753.7 y12-NH3^2/13.8ppm,y12-H2O+i^2/-1.5ppm -617.736 1000.9 ? -619.3562 112581.0 y5/0.0ppm -619.4061 1331.1 ? -620.3597 26856.2 y5+i/1.0ppm -625.3489 29725.9 y12^2/0.5ppm -625.8499 17686.6 y12+i^2/-0.2ppm -651.8593 1435.9 y13-H2O^2/-3.9ppm -660.8666 17322.8 y13^2/-0.8ppm -661.3691 10845.8 y13+i^2/0.8ppm -665.7083 857.4 ? -677.8406 865.0 ? -679.6729 1028.1 ? -692.6226 1839.8 ? -696.39 1380.5 y14^2/6.2ppm -696.8853 1825.9 y14+i^2/-2.6ppm -712.8559 1575.5 ? -729.4384 2131.4 y6-H2O/-3.0ppm -730.4251 3172.7 y6-NH3/0.6ppm -743.5792 878.1 ? -747.4517 51670.9 y6/0.7ppm -748.454 16389.8 y6+i/-0.1ppm -846.519 23172.3 y7/-0.7ppm -847.5219 8878.0 y7+i/-0.7ppm -888.9458 1103.0 ? -915.5491 1402.6 y8-H2O/8.8ppm -916.5312 1566.9 y8-NH3/6.7ppm,y8-H2O+i/-13.9ppm -933.5517 34961.3 y8/0.1ppm -934.5549 14638.2 y8+i/0.4ppm -962.5909 952.1 ? -967.9422 926.5 ? -1016.5936 1298.4 y9-H2O/4.8ppm -1017.5724 1109.4 y9-NH3/-0.3ppm,y9-H2O+i/-18.9ppm -1034.5992 17085.6 y9/-0.1ppm -1035.6008 7940.0 y9+i/-1.3ppm -1049.6464 924.5 ? -1068.5891 1068.8 ? -1072.3027 820.3 ? -1100.4142 824.6 ? -1121.6331 6228.7 y10/1.6ppm -1122.6238 3007.6 y10+i/-9.3ppm -1178.6527 11088.9 y11/-0.1ppm -1179.6552 6228.8 y11+i/-0.4ppm -1249.6901 2527.6 y12/0.2ppm -1250.6986 1715.0 y12+i/4.7ppm -1347.309 852.2 ? -1465.9084 1527.1 ? -1469.9915 925.5 ? - - -MS:1003061|library spectrum name=AAAALGSHGSCSSEVEK/2_1(10,C,CAM)_50eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=830.8834 -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[1]MS:1000045|collision energy=50 -[1]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=1185 -MS:1003203|constituent spectrum file="RO-QC-141112_Betenbaugh_HK_Fraction18.raw.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=2 -MS:1000002|sample name="betenbaugh_hk5" -MS:1000028|detector resolution=15000 -[2]MS:1000828|isolation window lower offset=0.95 -[2]UO:0000000|unit=MS:1000040|m/z -[3]MS:1000829|isolation window upper offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=30003.73 -MS:1003086|precursor apex intensity=28800.11 -MS:1000512|filter string="FTMS + p NSI d Full ms2 831.38@hcd34.00 [110.00-1675.00]" -MS:1003059|number of peaks=68 -[4]MS:1003275|other attribute name=Se -[4]MS:1003276|other attribute value=1(^G1:sc=6.94218e-013) - -MS:1000224|molecular mass=1661.7668 -MS:1000888|stripped peptide sequence=AAAALGSHGSCSSEVEK -MS:1000041|charge state=2 -[1]MS:1001975|delta m/z=4.1 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1003208|experimental precursor monoisotopic m/z=830.8868 -MS:1003169|proforma peptidoform sequence=AAAALGSHGSC[Carbamidomethyl]SSEVEK -MS:1001117|theoretical mass=1659.7522486039798 -[2]MS:1003048|number of enzymatic termini=2 -[2]MS:1001045|cleavage agent name=MS:1001251|Trypsin -[2]MS:1001112|n-terminal flanking residue=K -[2]MS:1001113|c-terminal flanking residue=E -[2]MS:1000885|protein accession="tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1" - -MS:1003079|total unassigned intensity fraction=0.4368 -MS:1003080|top 20 peak unassigned intensity fraction=0.184 -MS:1003289|intensity of highest unassigned peak=0.45 -MS:1003290|number of unassigned peaks among top 20 peaks=6 - -110.1102 57.808 ? -115.0864 84.449 a2/-1.6ppm -128.1915 60.078 ? -129.1023 157.87 IK/0.5ppm,y1-H2O/0.5ppm -130.0863 143.466 y1-NH3/0.4ppm -134.6533 64.924 ? -143.0814 409.786 b2/-0.7ppm -147.1131 319.305 y1/2.0ppm -151.4513 63.288 ? -153.7949 64.094 ? -159.3516 66.632 ? -165.1407 62.763 ? -185.7231 56.05 ? -192.253 56.668 ? -206.6181 58.523 ? -207.8363 67.364 ? -214.1188 604.289 b3/0.9ppm -240.1356 101.032 ? -242.2549 68.729 ? -252.7986 69.267 ? -257.1606 92.981 a4/-0.8ppm -258.144 282.108 y2-H2O/-3.2ppm -276.1561 234.148 y2/2.5ppm -282.3431 71.242 ? -285.1556 363.637 b4/-0.5ppm -312.7774 62.146 ? -343.4806 65.426 ? -355.0699 104.479 ? -370.4347 269.799 ? -375.2243 139.559 y3/1.3ppm -385.774 62.977 ? -388.1424 58.351 ? -431.0488 72.382 ? -529.347 83.459 ? -598.1849 62.213 ? -688.806 84.319 y13^2/-4.6ppm -692.6966 113.075 ? -694.6636 75.382 ? -700.6682 128.47 ? -725.4309 81.78 ? -817.4878 85.857 ? -819.1156 63.497 ? -903.9632 63.514 ? -982.4142 289.221 y9/-0.4ppm -983.42 122.064 b11/-16.6ppm,y9+i/2.6ppm -1036.3802 70.607 ? -1104.5166 70.543 ? -1119.4768 195.679 y10/2.9ppm -1120.4703 107.369 y10+i/-5.3ppm -1139.4911 84.154 b13-H2O/1.1ppm -1206.5106 83.121 y11/4.2ppm -1263.5344 229.989 y12/5.9ppm -1264.5262 152.204 y12+i/-2.8ppm -1268.5361 75.921 b14-H2O/2.9ppm -1286.5446 234.168 b14/1.3ppm -1287.5588 119.455 b14+i/10.2ppm -1376.6179 122.497 y13/5.0ppm -1376.9817 67.739 ? -1451.4869 67.46 ? -1465.7048 143.33 ? -1480.5077 95.07 ? -1522.3134 127.307 ? -1554.5259 83.112 ? -1595.7773 67.148 ? -1608.2555 61.797 ? -1623.9801 102.29 ? -1628.4393 118.77 ? -1670.2889 140.136 ? - - -MS:1003061|library spectrum name=AAAALGSHGSCSSEVEK/2_1(10,C,CAM)_52eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1003208|experimental precursor monoisotopic m/z=830.8834 -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[1]MS:1000045|collision energy=52 -[1]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=868 -MS:1003203|constituent spectrum file="RO-QC-141112_Betenbaugh_HK_Fraction19.raw.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=3 -MS:1000002|sample name="betenbaugh_hk2" -MS:1000028|detector resolution=15000 -[2]MS:1000828|isolation window lower offset=0.95 -[2]UO:0000000|unit=MS:1000040|m/z -[3]MS:1000829|isolation window upper offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=9544513.13 -MS:1003086|precursor apex intensity=26056925.91 -MS:1000512|filter string="FTMS + p NSI d Full ms2 830.88@hcd35.00 [140.00-1675.00]" -MS:1003059|number of peaks=402 -[4]MS:1003275|other attribute name=Se -[4]MS:1003276|other attribute value=1(^G1:sc=6.88234e-022) - -MS:1000224|molecular mass=1661.7668 -MS:1000888|stripped peptide sequence=AAAALGSHGSCSSEVEK -MS:1000041|charge state=2 -[1]MS:1001975|delta m/z=-2.0 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1003208|experimental precursor monoisotopic m/z=830.8817 -MS:1003169|proforma peptidoform sequence=AAAALGSHGSC[Carbamidomethyl]SSEVEK -MS:1001117|theoretical mass=1659.7522486039798 -[2]MS:1003048|number of enzymatic termini=2 -[2]MS:1001045|cleavage agent name=MS:1001251|Trypsin -[2]MS:1001112|n-terminal flanking residue=K -[2]MS:1001113|c-terminal flanking residue=E -[2]MS:1000885|protein accession="tr|G3HHY9|G3HHY9_CRIGR V-type proton ATPase subunit G 1 OS=Cricetulus griseus GN=I79_010250 PE=4 SV=1" - -MS:1003079|total unassigned intensity fraction=0.339 -MS:1003080|top 20 peak unassigned intensity fraction=0.0816 -MS:1003289|intensity of highest unassigned peak=0.17 -MS:1003290|number of unassigned peaks among top 20 peaks=3 - -141.1024 1824.4 ? -143.0816 54472.6 b2/0.7ppm -144.0851 2028.2 b2+i/5.6ppm -147.1129 40570.6 y1/0.7ppm -148.1159 2104.9 y1+i/1.9ppm -151.6119 866.7 ? -157.0613 1472.8 m12:13-H2O/3.4ppm -157.0974 1742.9 y1-H2O+CO/1.6ppm -157.1335 2797.4 ? -158.3324 771.5 ? -158.4784 915.0 ? -165.0449 784.1 ? -169.0973 19654.9 ? -170.1011 1507.2 ? -170.2729 987.0 ? -175.0683 1008.2 m12:13/-17.3ppm -182.0172 1038.4 ? -183.113 1337.8 ? -183.1501 1174.6 ? -185.1288 4333.2 ? -195.0881 4158.9 ? -196.1971 908.9 ? -196.9482 1078.6 ? -197.1034 2784.1 ? -199.0719 3248.0 ? -200.1024 1115.3 ? -201.1237 7050.8 ? -209.4671 931.3 ? -211.1448 5058.2 ? -213.1236 1676.9 ? -213.3639 815.5 ? -214.1189 134014.0 b3/1.3ppm -215.1223 10299.5 b3+i/4.2ppm -216.0974 817.8 ? -217.0823 3500.5 m13:14/1.9ppm -219.3852 836.0 ? -222.1242 2551.5 ? -225.0991 4462.1 ? -226.1194 1819.1 ? -229.1181 6277.7 m14:15/-0.8ppm,m15:16/-0.8ppm -234.0992 1302.3 ? -240.1345 21406.7 ? -240.2198 882.5 ? -241.1192 1989.1 y2-H2O-NH3/3.8ppm -241.1384 1684.0 ? -242.1143 4233.0 ? -242.1492 2778.4 ? -245.159 792.8 ? -246.0991 2154.2 ? -248.0698 1487.8 ? -249.5848 765.4 ? -254.1259 3540.4 ? -256.1303 1530.0 ? -256.1659 7535.6 ? -257.1612 23103.1 a4/1.5ppm -258.1451 53196.9 y2-H2O/1.0ppm -258.1656 1886.8 a4+i/7.9ppm -259.1288 853.6 y2-NH3/-0.2ppm -259.1489 5333.4 y2-H2O+i/4.5ppm -264.1097 4168.1 ? -271.1408 4874.5 ? -276.1557 43313.6 y2/1.1ppm -277.1596 3627.4 y2+i/4.7ppm -282.1198 11960.0 ? -282.1816 6243.1 ? -285.156 70721.5 b4/0.9ppm -286.1596 8357.3 b4+i/3.8ppm -287.0818 1676.5 ? -297.1559 2764.6 ? -299.2081 5654.7 ? -301.1155 1445.2 ? -304.1141 3271.6 ? -313.1878 2255.8 ? -317.2701 1126.7 ? -327.1668 2255.7 ? -327.2031 12335.3 ? -328.2078 1419.9 ? -335.1022 1102.7 ? -339.1418 3562.0 ? -339.2035 4082.1 ? -342.1779 5278.6 ? -349.2 1115.0 ? -353.2187 6849.9 ? -355.1979 2456.3 ? -356.2301 1374.8 ? -358.1734 2130.2 ? -367.2096 3137.8 ? -369.1535 1179.9 ? -370.2455 9499.6 a5/1.7ppm -371.7008 1451.4 ? -375.2245 22737.7 y3/1.8ppm -376.2279 2902.4 y3+i/3.1ppm -377.1941 3243.0 ? -382.2082 1160.7 ? 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a/implementations/python/tests/test_data/clusters_example.mzlb +++ /dev/null @@ -1,142 +0,0 @@ - - -MS:1003320|spectrum cluster size=6 -MS:1003268|spectrum cluster member spectrum keys=1,6,23,63,89 -MS:1003269|spectrum cluster member USI=mzspec:PXD000561:Adult_Frontalcortex_bRP_Elite_85_f09:scan:17555 -[1]MS:1003321|summary statistics of clustered spectra=MS:1003304|spectral dot product -[1]MS:1003176|attribute mean=0.7 -[2]MS:1003321|summary statistics of clustered spectra=MS:1003208|experimental precursor monoisotopic m/z -[2]MS:1003176|attribute mean=1029.05 -[2]MS:1003177|attribute standard deviation=0.41 -MS:1003322|spectrum cluster best representative=63 - - -MS:1003061|library spectrum name=AAAACALTPGPLADLAAR/2_1(4,C,CAM)_46eV -MS:1003065|spectrum aggregation type=MS:1003066|singleton spectrum -MS:1000041|charge state=2 -MS:1000744|selected ion m/z=855.4538 -MS:1000044|dissociation method=MS:1000422|beam-type collision-induced dissociation -[1]MS:1000045|collision energy=46 -[1]UO:0000000|unit=UO:0000266|electronvolt -MS:1003057|scan number=5538 -MS:1003203|constituent spectrum file="CHO-K1_bRPLC_C1.RAW.FT.hcd.ch.MGF" -MS:1003070|number of replicate spectra used=1 -MS:1003069|number of replicate spectra available=2 -MS:1000002|sample name="jhu_cho_brplc_cam" -MS:1000028|detector resolution=7500 -[2]MS:1000828|isolation window lower offset=0.95 -[2]UO:0000000|unit=MS:1000040|m/z -[3]MS:1000829|isolation window upper offset=0.95 -[3]UO:0000000|unit=MS:1000040|m/z -MS:1003085|previous MS1 scan precursor intensity=8799173.32 -MS:1003086|precursor apex intensity=25273307.5 -MS:1000512|filter string="FTMS + p NSI d Full ms2 855.96@hcd35.00 [140.00-1725.00]" -MS:1003059|number of peaks=87 -[4]MS:1003275|other attribute name=Se -[4]MS:1003276|other attribute value=1(^G1:sc=8.13346e-015) - -MS:1000224|molecular mass=1710.9076 -MS:1000888|stripped peptide sequence=AAAACALTPGPLADLAAR -[1]MS:1001975|delta m/z=1.4 -[1]UO:0000000|unit=UO:0000169|parts per million -MS:1003208|experimental precursor monoisotopic m/z=855.455 -MS:1003169|proforma peptidoform sequence=AAAAC[Carbamidomethyl]ALTPGPLADLAAR -MS:1001117|theoretical mass=1708.89303961159 -[2]MS:1003048|number of enzymatic termini=2 -[2]MS:1001045|cleavage agent name=MS:1001251|Trypsin -[2]MS:1001112|n-terminal flanking residue=R -[2]MS:1001113|c-terminal flanking residue=L -[2]MS:1000885|protein accession="tr|G3IJB9|G3IJB9_CRIGR UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 OS=Cricetulus griseus GN=I79_023952 PE=4 SV=1" - -MS:1003079|total unassigned intensity fraction=0.2848 -MS:1003080|top 20 peak unassigned intensity fraction=0.1879 -MS:1003289|intensity of highest unassigned peak=0.45 -MS:1003290|number of unassigned peaks among top 20 peaks=4 - -143.0823 14791.5 b2/5.6ppm -153.2575 5008.6 ? -159.0917 11531.8 ? -162.5977 5804.6 ? -169.0972 12931.0 ? -175.1193 18211.1 y1/2.0ppm,IR/2.0ppm -194.0699 6011.0 ? -199.1074 6737.4 ? -201.7527 5576.3 ? -212.1051 13786.1 ? -214.1195 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b/implementations/python/tests/test_data/complex_interpretations.mzlb.txt deleted file mode 100644 index bc547e5..0000000 --- a/implementations/python/tests/test_data/complex_interpretations.mzlb.txt +++ /dev/null @@ -1,15 +0,0 @@ - -MS:1003061|library spectrum name=Test -MS:1000744|selected ion m/z=880.8902 - -MS:1000888|peptidoform=DSDDVPM[Oxidation]VLVGNKCDLAAR - -MS:1000888|peptidoform=VLVGNKCDLDSDDVPMVLR - -MS:1000888|peptidoform=CDLDSDDSDDVPMVLSAR - -MS:1003163|analyte mixture members=1,2 -MS:1002357|PSM-level probability=0.974 - -MS:1003163|analyte mixture members=3 -MS:1002357|PSM-level probability=0.937 diff --git a/implementations/python/tests/test_data/complex_interpretations_with_members.mzlb.json b/implementations/python/tests/test_data/complex_interpretations_with_members.mzlb.json deleted file mode 100644 index 8fe0aee..0000000 --- a/implementations/python/tests/test_data/complex_interpretations_with_members.mzlb.json +++ /dev/null @@ -1,141 +0,0 @@ -{ - "analyte_attribute_sets": { - "all": [] - }, - "attributes": [], - "clusters": [], - "format_version": "1.0", - "interpretation_attribute_sets": { - "all": [] - }, - "spectra": [ - { - "analytes": { - "1": { - "attributes": [ - { - "accession": "MS:1000888", - "name": "peptidoform", - "value": "DSDDVPM[Oxidation]VLVGNKCDLAAR" - } - ], - "id": "1" - }, - "2": { - "attributes": [ - { - "accession": "MS:1000888", - "name": "peptidoform", - "value": "VLVGNKCDLDSDDVPMVLR" - } - ], - "id": "2" - }, - "3": { - "attributes": [ - { - "accession": "MS:1000888", - "name": "peptidoform", - "value": "CDLDSDDSDDVPMVLSAR" - } - ], - "id": "3" - } - }, - "attributes": [ - { - "accession": "MS:1003237", - "name": "library spectrum key", - "value": 1 - }, - { - "accession": "MS:1003061", - "name": "library spectrum name", - "value": "Test" - }, - { - "accession": "MS:1000744", - "name": "selected ion m/z", - "value": 880.8902 - } - ], - "intensities": [], - "interpretations": { - "1": { - "attributes": [ - { - "accession": "MS:1002357", - "name": "PSM-level probability", - "value": 0.974 - }, - { - "accession": "MS:1003163", - "name": "analyte mixture members", - "value": [ - 1, - 2 - ] - } - ], - "id": "1", - "members": { - "1": { - "attributes": [ - { - "accession": "MS:XXXXXXX", - "name": "explained intensity fraction", - "value": 0.287 - } - ], - "id": "1" - }, - "2": { - "attributes": [ - { - "accession": "MS:XXXXXXX", - "name": "explained intensity fraction", - "value": 0.423 - } - ], - "id": "2" - } - } - }, - "2": { - "attributes": [ - { - "accession": "MS:1002357", - "name": "PSM-level probability", - "value": 0.937 - }, - { - "accession": "MS:1003163", - "name": "analyte mixture members", - "value": [ - 3 - ] - } - ], - "id": "2", - "members": { - "3": { - "attributes": [ - { - "accession": "MS:XXXXXXX", - "name": "explained intensity fraction", - "value": 0.512 - } - ], - "id": "3" - } - } - } - }, - "mzs": [], - "peak_annotations": [] - } - ], - "spectrum_attribute_sets": { - "all": [] - } -} \ No newline at end of file diff --git a/implementations/python/tests/test_data/complex_interpretations_with_members.mzlb.txt b/implementations/python/tests/test_data/complex_interpretations_with_members.mzlb.txt deleted file mode 100644 index 5d648a9..0000000 --- a/implementations/python/tests/test_data/complex_interpretations_with_members.mzlb.txt +++ /dev/null @@ -1,21 +0,0 @@ - -MS:1003061|library spectrum name=Test -MS:1000744|selected ion m/z=880.8902 - -MS:1000888|peptidoform=DSDDVPM[Oxidation]VLVGNKCDLAAR - -MS:1000888|peptidoform=VLVGNKCDLDSDDVPMVLR - -MS:1000888|peptidoform=CDLDSDDSDDVPMVLSAR - -MS:1002357|PSM-level probability=0.974 -MS:1003163|analyte mixture members=1,2 - -MS:XXXXXXX|explained intensity fraction=0.287 - -MS:XXXXXXX|explained intensity fraction=0.423 - -MS:1002357|PSM-level probability=0.937 -MS:1003163|analyte mixture members=3 - -MS:XXXXXXX|explained intensity fraction=0.512 diff --git a/implementations/python/tests/test_data/generate_annotations.py b/implementations/python/tests/test_data/generate_annotations.py deleted file mode 100644 index 14ee290..0000000 --- a/implementations/python/tests/test_data/generate_annotations.py +++ /dev/null @@ -1,21 +0,0 @@ -import os - -from mzlib import SpectrumLibrary -from mzlib import annotation - -workspace = os.path.dirname(__file__) - -source = SpectrumLibrary(filename=os.path.join( - workspace, "chinese_hamster_hcd_selected_head.msp")) -print(source) -annots = set() -for spec in source: - print(spec.name) - for peak in spec.peak_list: - for a in peak[2]: - if isinstance(a, annotation.InvalidAnnotation): - breakpoint() - annots.add(a) - -with open(os.path.join(workspace, "annotations.txt"), 'wt') as fh: - fh.write("\n".join(sorted(map(str, annots)))) diff --git a/implementations/python/tests/test_data/human_serum.head.spectronaut.tsv b/implementations/python/tests/test_data/human_serum.head.spectronaut.tsv deleted file mode 100644 index 55db2fb..0000000 --- a/implementations/python/tests/test_data/human_serum.head.spectronaut.tsv +++ /dev/null @@ -1,145 +0,0 @@ -ReferenceRun PrecursorCharge Workflow IntModifiedPeptide CV AllowForNormalization ModifiedPeptide StrippedPeptide iRT IonMobility iRTSourceSpecific BGSInferenceId IsProteotypic IntLabeledPeptide LabeledPeptide PrecursorMz ReferenceRunQvalue ReferenceRunMS1Response FragmentLossType FragmentNumber FragmentType FragmentCharge FragmentMz RelativeIntensity ExcludeFromAssay Database ProteinGroups UniProtIds Protein Name ProteinDescription Organisms OrganismId Genes Protein Existence Sequence Version FASTAName -IK_221028_C19_lib2_01 2 _AQIPILR_ -60 TRUE _AQIPILR_ AQIPILR 28.658491 0.7629655 28.450514|28.82925 P04114 TRUE _AQIPILR_ _AQIPILR_ 405.7634379 0.006434474 11824944 noloss 3 b 1 313.1870317 3.564491 FALSE sp P04114 P04114 APOB_HUMAN Apolipoprotein B-100 Homo sapiens 9606 APOB 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AQIPILR_ -60 TRUE _AQIPILR_ AQIPILR 28.658491 0.7629655 28.450514|28.82925 P04114 TRUE _AQIPILR_ _AQIPILR_ 405.7634379 0.006434474 11824944 noloss 3 y 1 401.2870801 3.3441753 FALSE sp P04114 P04114 APOB_HUMAN Apolipoprotein B-100 Homo sapiens 9606 APOB 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AQIPILR_ -60 TRUE _AQIPILR_ AQIPILR 28.658491 0.7629655 28.450514|28.82925 P04114 TRUE _AQIPILR_ _AQIPILR_ 405.7634379 0.006434474 11824944 noloss 4 y 1 498.339844 100 FALSE sp P04114 P04114 APOB_HUMAN Apolipoprotein B-100 Homo sapiens 9606 APOB 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AQIPILR_ -60 TRUE _AQIPILR_ AQIPILR 28.658491 0.7629655 28.450514|28.82925 P04114 TRUE _AQIPILR_ _AQIPILR_ 405.7634379 0.006434474 11824944 noloss 4 y 2 249.6735602 11.528888 FALSE sp P04114 P04114 APOB_HUMAN Apolipoprotein B-100 Homo sapiens 9606 APOB 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AQIPILR_ -60 TRUE _AQIPILR_ AQIPILR 28.658491 0.7629655 28.450514|28.82925 P04114 TRUE _AQIPILR_ _AQIPILR_ 405.7634379 0.006434474 11824944 noloss 5 y 1 611.423908 36.853043 FALSE sp P04114 P04114 APOB_HUMAN Apolipoprotein B-100 Homo sapiens 9606 APOB 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AQIPILR_ -60 TRUE _AQIPILR_ AQIPILR 28.658491 0.7629655 28.450514|28.82925 P04114 TRUE _AQIPILR_ _AQIPILR_ 405.7634379 0.006434474 11824944 NH3 4 y 1 481.3132956 5.708535 FALSE sp P04114 P04114 APOB_HUMAN Apolipoprotein B-100 Homo sapiens 9606 APOB 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AGVLFGMSDR_ -40 TRUE _AGVLFGMSDR_ AGVLFGMSDR 46.12812 0.8644136 46.12812|44.301308 P09172 TRUE _AGVLFGMSDR_ _AGVLFGMSDR_ 526.763309 0.000140481 1200641 noloss 3 b 1 228.1342679 48.582985 FALSE sp P09172 P09172 DOPO_HUMAN Dopamine beta-hydroxylase Homo sapiens 9606 DBH 1 3 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AGVLFGMSDR_ -40 TRUE _AGVLFGMSDR_ AGVLFGMSDR 46.12812 0.8644136 46.12812|44.301308 P09172 TRUE _AGVLFGMSDR_ _AGVLFGMSDR_ 526.763309 0.000140481 1200641 noloss 3 y 1 377.1779236 4.8015785 FALSE sp P09172 P09172 DOPO_HUMAN Dopamine beta-hydroxylase Homo sapiens 9606 DBH 1 3 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AGVLFGMSDR_ -40 TRUE _AGVLFGMSDR_ AGVLFGMSDR 46.12812 0.8644136 46.12812|44.301308 P09172 TRUE _AGVLFGMSDR_ _AGVLFGMSDR_ 526.763309 0.000140481 1200641 noloss 4 b 1 341.2183319 4.1744895 TRUE sp P09172 P09172 DOPO_HUMAN Dopamine beta-hydroxylase Homo sapiens 9606 DBH 1 3 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AGVLFGMSDR_ -40 TRUE _AGVLFGMSDR_ AGVLFGMSDR 46.12812 0.8644136 46.12812|44.301308 P09172 TRUE _AGVLFGMSDR_ _AGVLFGMSDR_ 526.763309 0.000140481 1200641 noloss 4 y 1 508.2184085 5.056169 FALSE sp P09172 P09172 DOPO_HUMAN Dopamine beta-hydroxylase Homo sapiens 9606 DBH 1 3 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AGVLFGMSDR_ -40 TRUE _AGVLFGMSDR_ AGVLFGMSDR 46.12812 0.8644136 46.12812|44.301308 P09172 TRUE _AGVLFGMSDR_ _AGVLFGMSDR_ 526.763309 0.000140481 1200641 noloss 5 y 1 565.2398722 69.96272 FALSE sp P09172 P09172 DOPO_HUMAN Dopamine beta-hydroxylase Homo sapiens 9606 DBH 1 3 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AGVLFGMSDR_ -40 TRUE _AGVLFGMSDR_ AGVLFGMSDR 46.12812 0.8644136 46.12812|44.301308 P09172 TRUE _AGVLFGMSDR_ _AGVLFGMSDR_ 526.763309 0.000140481 1200641 noloss 6 y 1 712.3082861 100 FALSE sp P09172 P09172 DOPO_HUMAN Dopamine beta-hydroxylase Homo sapiens 9606 DBH 1 3 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AGVLFGMSDR_ -40 TRUE _AGVLFGMSDR_ AGVLFGMSDR 46.12812 0.8644136 46.12812|44.301308 P09172 TRUE _AGVLFGMSDR_ _AGVLFGMSDR_ 526.763309 0.000140481 1200641 noloss 7 y 1 825.3923501 51.118713 FALSE sp P09172 P09172 DOPO_HUMAN Dopamine beta-hydroxylase Homo sapiens 9606 DBH 1 3 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AGVLFGMSDR_ -40 TRUE _AGVLFGMSDR_ AGVLFGMSDR 46.12812 0.8644136 46.12812|44.301308 P09172 TRUE _AGVLFGMSDR_ _AGVLFGMSDR_ 526.763309 0.000140481 1200641 noloss 8 y 1 924.460764 1.5956572 TRUE sp P09172 P09172 DOPO_HUMAN Dopamine beta-hydroxylase Homo sapiens 9606 DBH 1 3 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AGVLFGMSDR_ -40 TRUE _AGVLFGMSDR_ AGVLFGMSDR 46.12812 0.8644136 46.12812|44.301308 P09172 TRUE _AGVLFGMSDR_ _AGVLFGMSDR_ 526.763309 0.000140481 1200641 NH3 3 y 1 360.1513752 3.1122544 TRUE sp P09172 P09172 DOPO_HUMAN Dopamine beta-hydroxylase Homo sapiens 9606 DBH 1 3 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AGVLFGMSDR_ -40 TRUE _AGVLFGMSDR_ AGVLFGMSDR 46.12812 0.8644136 46.12812|44.301308 P09172 TRUE _AGVLFGMSDR_ _AGVLFGMSDR_ 526.763309 0.000140481 1200641 NH3 4 y 1 491.1918601 1.0637656 TRUE sp P09172 P09172 DOPO_HUMAN Dopamine beta-hydroxylase Homo sapiens 9606 DBH 1 3 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AGVLFGMSDR_ -40 TRUE _AGVLFGMSDR_ AGVLFGMSDR 46.12812 0.8644136 46.12812|44.301308 P09172 TRUE _AGVLFGMSDR_ _AGVLFGMSDR_ 526.763309 0.000140481 1200641 H2O 6 y 1 694.2977213 1.3498487 TRUE sp P09172 P09172 DOPO_HUMAN Dopamine beta-hydroxylase Homo sapiens 9606 DBH 1 3 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AGVLFGMSDR_ -40 TRUE _AGVLFGMSDR_ AGVLFGMSDR 46.12812 0.8644136 46.12812|44.301308 P09172 TRUE _AGVLFGMSDR_ _AGVLFGMSDR_ 526.763309 0.000140481 1200641 NH3 6 y 1 695.2817378 2.9444132 TRUE sp P09172 P09172 DOPO_HUMAN Dopamine beta-hydroxylase Homo sapiens 9606 DBH 1 3 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _AGVLFGMSDR_ -40 TRUE _AGVLFGMSDR_ AGVLFGMSDR 46.12812 0.8644136 46.12812|44.301308 P09172 TRUE _AGVLFGMSDR_ _AGVLFGMSDR_ 526.763309 0.000140481 1200641 H2O 3 y 1 359.1673588 2.1920948 TRUE sp P09172 P09172 DOPO_HUMAN Dopamine beta-hydroxylase Homo sapiens 9606 DBH 1 3 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 noloss 3 b 1 360.1037556 14.370086 TRUE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 noloss 3 y 1 377.2030757 69.91263 FALSE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 noloss 4 y 1 490.2871397 47.727154 FALSE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 noloss 5 b 1 588.1896105 3.50105 TRUE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 noloss 5 y 1 603.3712037 20.282309 FALSE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 noloss 6 b 1 701.2736745 4.035067 TRUE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 noloss 6 y 1 717.4141311 24.80533 FALSE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 noloss 7 y 1 831.4570586 21.473965 FALSE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 noloss 8 y 1 946.4840016 100 FALSE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 H2O 3 b 1 342.0931908 5.760026 TRUE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 H2O 3 y 1 359.1925109 5.090061 TRUE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 H2O 4 y 1 472.2765749 4.874231 TRUE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 NH3 5 b 1 571.1630621 4.1113725 TRUE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 NH3 6 b 1 684.2471261 4.05031 TRUE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 NH3 6 y 1 700.3875827 3.518 TRUE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 NH3 7 y 1 814.4305102 7.3916 TRUE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 H2O 8 y 1 928.4734368 5.1134515 TRUE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 NH3 8 y 1 929.4574532 10.1338825 TRUE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _DEDNNLLTEK_ -40 TRUE _DEDNNLLTEK_ DEDNNLLTEK 13.850179 0.90230334 26.061718|13.850179 P09486 TRUE _DEDNNLLTEK_ _DEDNNLLTEK_ 595.7804071 0.000191886 313203.16 noloss 9 y 1 1075.526595 14.727533 TRUE sp P09486 P09486 SPRC_HUMAN SPARC Homo sapiens 9606 SPARC 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _GWVTDGFSSLK_ -40 TRUE _GWVTDGFSSLK_ GWVTDGFSSLK 62.688942 0.92365193 62.87711|62.59508 P02656 TRUE _GWVTDGFSSLK_ _GWVTDGFSSLK_ 598.8009456 0.000448056 9233573 noloss 3 b 1 343.1764671 3.8687427 TRUE sp P02656 P02656 APOC3_HUMAN Apolipoprotein C-III Homo sapiens 9606 APOC3 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _GWVTDGFSSLK_ -40 TRUE _GWVTDGFSSLK_ GWVTDGFSSLK 62.688942 0.92365193 62.87711|62.59508 P02656 TRUE _GWVTDGFSSLK_ _GWVTDGFSSLK_ 598.8009456 0.000448056 9233573 noloss 3 y 1 347.2288965 6.1732 FALSE sp P02656 P02656 APOC3_HUMAN Apolipoprotein C-III Homo sapiens 9606 APOC3 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _GWVTDGFSSLK_ -40 TRUE _GWVTDGFSSLK_ GWVTDGFSSLK 62.688942 0.92365193 62.87711|62.59508 P02656 TRUE _GWVTDGFSSLK_ _GWVTDGFSSLK_ 598.8009456 0.000448056 9233573 noloss 4 b 1 444.2241455 1.421 TRUE sp P02656 P02656 APOC3_HUMAN Apolipoprotein C-III Homo sapiens 9606 APOC3 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _GWVTDGFSSLK_ -40 TRUE _GWVTDGFSSLK_ GWVTDGFSSLK 62.688942 0.92365193 62.87711|62.59508 P02656 TRUE _GWVTDGFSSLK_ _GWVTDGFSSLK_ 598.8009456 0.000448056 9233573 noloss 4 y 1 434.260925 9.774844 FALSE sp P02656 P02656 APOC3_HUMAN Apolipoprotein C-III Homo sapiens 9606 APOC3 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _GWVTDGFSSLK_ -40 TRUE _GWVTDGFSSLK_ GWVTDGFSSLK 62.688942 0.92365193 62.87711|62.59508 P02656 TRUE _GWVTDGFSSLK_ _GWVTDGFSSLK_ 598.8009456 0.000448056 9233573 noloss 5 y 1 581.3293389 2.66143 TRUE sp P02656 P02656 APOC3_HUMAN Apolipoprotein C-III Homo sapiens 9606 APOC3 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _GWVTDGFSSLK_ -40 TRUE _GWVTDGFSSLK_ GWVTDGFSSLK 62.688942 0.92365193 62.87711|62.59508 P02656 TRUE _GWVTDGFSSLK_ _GWVTDGFSSLK_ 598.8009456 0.000448056 9233573 noloss 6 y 1 638.3508026 19.109653 FALSE sp P02656 P02656 APOC3_HUMAN Apolipoprotein C-III Homo sapiens 9606 APOC3 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _GWVTDGFSSLK_ -40 TRUE _GWVTDGFSSLK_ GWVTDGFSSLK 62.688942 0.92365193 62.87711|62.59508 P02656 TRUE _GWVTDGFSSLK_ _GWVTDGFSSLK_ 598.8009456 0.000448056 9233573 noloss 7 y 1 753.3777456 20.841564 FALSE sp P02656 P02656 APOC3_HUMAN Apolipoprotein C-III Homo sapiens 9606 APOC3 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _GWVTDGFSSLK_ -40 TRUE _GWVTDGFSSLK_ GWVTDGFSSLK 62.688942 0.92365193 62.87711|62.59508 P02656 TRUE _GWVTDGFSSLK_ _GWVTDGFSSLK_ 598.8009456 0.000448056 9233573 noloss 8 y 1 854.4254241 60.931602 FALSE sp P02656 P02656 APOC3_HUMAN Apolipoprotein C-III Homo sapiens 9606 APOC3 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _GWVTDGFSSLK_ -40 TRUE _GWVTDGFSSLK_ GWVTDGFSSLK 62.688942 0.92365193 62.87711|62.59508 P02656 TRUE _GWVTDGFSSLK_ _GWVTDGFSSLK_ 598.8009456 0.000448056 9233573 noloss 9 y 1 953.493838 36.67316 FALSE sp P02656 P02656 APOC3_HUMAN Apolipoprotein C-III Homo sapiens 9606 APOC3 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _GWVTDGFSSLK_ -40 TRUE _GWVTDGFSSLK_ GWVTDGFSSLK 62.688942 0.92365193 62.87711|62.59508 P02656 TRUE _GWVTDGFSSLK_ _GWVTDGFSSLK_ 598.8009456 0.000448056 9233573 H2O 4 y 1 416.2503601 2.702636 TRUE sp P02656 P02656 APOC3_HUMAN Apolipoprotein C-III Homo sapiens 9606 APOC3 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _GWVTDGFSSLK_ -40 TRUE _GWVTDGFSSLK_ GWVTDGFSSLK 62.688942 0.92365193 62.87711|62.59508 P02656 TRUE _GWVTDGFSSLK_ _GWVTDGFSSLK_ 598.8009456 0.000448056 9233573 H2O 7 y 1 735.3671808 2.1958628 TRUE sp P02656 P02656 APOC3_HUMAN Apolipoprotein C-III Homo sapiens 9606 APOC3 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _GWVTDGFSSLK_ -40 TRUE _GWVTDGFSSLK_ GWVTDGFSSLK 62.688942 0.92365193 62.87711|62.59508 P02656 TRUE _GWVTDGFSSLK_ _GWVTDGFSSLK_ 598.8009456 0.000448056 9233573 H2O 8 y 1 836.4148593 4.374068 TRUE sp P02656 P02656 APOC3_HUMAN Apolipoprotein C-III Homo sapiens 9606 APOC3 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _GWVTDGFSSLK_ -40 TRUE _GWVTDGFSSLK_ GWVTDGFSSLK 62.688942 0.92365193 62.87711|62.59508 P02656 TRUE _GWVTDGFSSLK_ _GWVTDGFSSLK_ 598.8009456 0.000448056 9233573 H2O 9 y 1 935.4832732 4.7364564 TRUE sp P02656 P02656 APOC3_HUMAN Apolipoprotein C-III Homo sapiens 9606 APOC3 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _GWVTDGFSSLK_ -40 TRUE _GWVTDGFSSLK_ GWVTDGFSSLK 62.688942 0.92365193 62.87711|62.59508 P02656 TRUE _GWVTDGFSSLK_ _GWVTDGFSSLK_ 598.8009456 0.000448056 9233573 H2O 9 y 2 468.2452748 1.662614 TRUE sp P02656 P02656 APOC3_HUMAN Apolipoprotein C-III Homo sapiens 9606 APOC3 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 noloss 3 b 1 288.1553973 13.402388 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 noloss 3 y 1 374.2397956 35.40592 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 noloss 4 y 1 560.3191085 46.133404 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 noloss 5 y 1 675.3460516 49.92076 FALSE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 noloss 6 y 1 803.4046291 88.30317 FALSE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 noloss 7 y 1 916.488693 35.01724 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 noloss 7 y 2 458.7479848 8.279677 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 noloss 8 y 1 1003.520721 100 FALSE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 noloss 9 y 1 1104.5684 49.551434 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 H2O 3 b 1 270.1448324 95.16555 FALSE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 H2O 6 y 1 785.3940643 24.796286 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 H2O 6 y 2 393.2006704 13.1079035 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 NH3 6 y 1 786.3780807 46.45572 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 H2O 8 y 1 985.5101566 7.3205233 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 H2O 8 y 2 493.2587166 4.255348 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 H2O 9 y 1 1086.557835 7.42398 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 noloss 4 b 2 201.1233688 88.65463 FALSE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 noloss 4 b 1 401.2394612 4.14027 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 noloss 9 y 2 552.7878382 4.422511 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 H2O 4 b 1 383.2288964 12.326735 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 NH3 8 y 1 986.4941731 24.063145 TRUE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _VTSIQDWVQK_ -40 TRUE _VTSIQDWVQK_ VTSIQDWVQK 39.73143 0.9102522 39.839462|39.662376 P00738 TRUE _VTSIQDWVQK_ _VTSIQDWVQK_ 602.3220451 0.000163706 907266.44 NH3 3 y 1 357.2132472 60.34427 FALSE sp P00738 P00738 HPT_HUMAN Haptoglobin Homo sapiens 9606 HP 1 1 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _QELSEAEQATR_ -40 TRUE _QELSEAEQATR_ QELSEAEQATR -14.638051 0.92576075 -14.638051|-17.592121 P01024 TRUE _QELSEAEQATR_ _QELSEAEQATR_ 631.3045807 0 1612831.6 noloss 3 b 1 371.192511 3.1688333 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _QELSEAEQATR_ -40 TRUE _QELSEAEQATR_ QELSEAEQATR -14.638051 0.92576075 -14.638051|-17.592121 P01024 TRUE _QELSEAEQATR_ _QELSEAEQATR_ 631.3045807 0 1612831.6 noloss 3 y 1 347.2037444 10.465045 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _QELSEAEQATR_ -40 TRUE _QELSEAEQATR_ QELSEAEQATR -14.638051 0.92576075 -14.638051|-17.592121 P01024 TRUE _QELSEAEQATR_ _QELSEAEQATR_ 631.3045807 0 1612831.6 noloss 4 y 1 475.2623219 23.276728 FALSE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _QELSEAEQATR_ -40 TRUE _QELSEAEQATR_ QELSEAEQATR -14.638051 0.92576075 -14.638051|-17.592121 P01024 TRUE _QELSEAEQATR_ _QELSEAEQATR_ 631.3045807 0 1612831.6 noloss 5 y 1 604.304915 37.09764 FALSE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _QELSEAEQATR_ -40 TRUE _QELSEAEQATR_ QELSEAEQATR -14.638051 0.92576075 -14.638051|-17.592121 P01024 TRUE _QELSEAEQATR_ _QELSEAEQATR_ 631.3045807 0 1612831.6 noloss 6 y 1 675.3420288 64.2233 FALSE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _QELSEAEQATR_ -40 TRUE _QELSEAEQATR_ QELSEAEQATR -14.638051 0.92576075 -14.638051|-17.592121 P01024 TRUE _QELSEAEQATR_ _QELSEAEQATR_ 631.3045807 0 1612831.6 noloss 7 y 1 804.3846219 37.812637 FALSE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _QELSEAEQATR_ -40 TRUE _QELSEAEQATR_ QELSEAEQATR -14.638051 0.92576075 -14.638051|-17.592121 P01024 TRUE _QELSEAEQATR_ _QELSEAEQATR_ 631.3045807 0 1612831.6 noloss 8 y 1 891.4166503 96.74726 FALSE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _QELSEAEQATR_ -40 TRUE _QELSEAEQATR_ QELSEAEQATR -14.638051 0.92576075 -14.638051|-17.592121 P01024 TRUE _QELSEAEQATR_ _QELSEAEQATR_ 631.3045807 0 1612831.6 noloss 9 y 1 1004.500714 100 FALSE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _QELSEAEQATR_ -40 TRUE _QELSEAEQATR_ QELSEAEQATR -14.638051 0.92576075 -14.638051|-17.592121 P01024 TRUE _QELSEAEQATR_ _QELSEAEQATR_ 631.3045807 0 1612831.6 H2O 3 b 1 353.1819462 4.8028316 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _QELSEAEQATR_ -40 TRUE _QELSEAEQATR_ QELSEAEQATR -14.638051 0.92576075 -14.638051|-17.592121 P01024 TRUE _QELSEAEQATR_ _QELSEAEQATR_ 631.3045807 0 1612831.6 NH3 3 b 1 354.1659627 5.46505 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _QELSEAEQATR_ -40 TRUE _QELSEAEQATR_ QELSEAEQATR -14.638051 0.92576075 -14.638051|-17.592121 P01024 TRUE _QELSEAEQATR_ _QELSEAEQATR_ 631.3045807 0 1612831.6 NH3 4 y 1 458.2357735 1.8879279 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _QELSEAEQATR_ -40 TRUE _QELSEAEQATR_ QELSEAEQATR -14.638051 0.92576075 -14.638051|-17.592121 P01024 TRUE _QELSEAEQATR_ _QELSEAEQATR_ 631.3045807 0 1612831.6 NH3 6 y 1 658.3154804 1.120537 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _QELSEAEQATR_ -40 TRUE _QELSEAEQATR_ QELSEAEQATR -14.638051 0.92576075 -14.638051|-17.592121 P01024 TRUE _QELSEAEQATR_ _QELSEAEQATR_ 631.3045807 0 1612831.6 H2O 7 y 1 786.3740571 7.649042 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _QELSEAEQATR_ -40 TRUE _QELSEAEQATR_ QELSEAEQATR -14.638051 0.92576075 -14.638051|-17.592121 P01024 TRUE _QELSEAEQATR_ _QELSEAEQATR_ 631.3045807 0 1612831.6 H2O 8 y 1 873.4060855 4.228747 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _QELSEAEQATR_ -40 TRUE _QELSEAEQATR_ QELSEAEQATR -14.638051 0.92576075 -14.638051|-17.592121 P01024 TRUE _QELSEAEQATR_ _QELSEAEQATR_ 631.3045807 0 1612831.6 H2O 9 y 1 986.4901495 1.3095266 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _EEGTDLEVTANR_ -40 TRUE _EEGTDLEVTANR_ EEGTDLEVTANR 5.3526073 0.94296074 5.3526073|3.901706 P20742 TRUE _EEGTDLEVTANR_ _EEGTDLEVTANR_ 667.3151454 0.000139519 230759.89 noloss 3 y 1 360.1989934 20.52395 TRUE sp P20742 P20742 PZP_HUMAN Pregnancy zone protein Homo sapiens 9606 PZP 1 4 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _EEGTDLEVTANR_ -40 TRUE _EEGTDLEVTANR_ EEGTDLEVTANR 5.3526073 0.94296074 5.3526073|3.901706 P20742 TRUE _EEGTDLEVTANR_ _EEGTDLEVTANR_ 667.3151454 0.000139519 230759.89 noloss 4 y 1 461.2466719 85.759026 FALSE sp P20742 P20742 PZP_HUMAN Pregnancy zone protein Homo sapiens 9606 PZP 1 4 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _EEGTDLEVTANR_ -40 TRUE _EEGTDLEVTANR_ EEGTDLEVTANR 5.3526073 0.94296074 5.3526073|3.901706 P20742 TRUE _EEGTDLEVTANR_ _EEGTDLEVTANR_ 667.3151454 0.000139519 230759.89 noloss 5 y 1 560.3150858 82.32931 FALSE sp P20742 P20742 PZP_HUMAN Pregnancy zone protein Homo sapiens 9606 PZP 1 4 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _EEGTDLEVTANR_ -40 TRUE _EEGTDLEVTANR_ EEGTDLEVTANR 5.3526073 0.94296074 5.3526073|3.901706 P20742 TRUE _EEGTDLEVTANR_ _EEGTDLEVTANR_ 667.3151454 0.000139519 230759.89 noloss 6 y 1 689.3576789 100 FALSE sp P20742 P20742 PZP_HUMAN Pregnancy zone protein Homo sapiens 9606 PZP 1 4 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _EEGTDLEVTANR_ -40 TRUE _EEGTDLEVTANR_ EEGTDLEVTANR 5.3526073 0.94296074 5.3526073|3.901706 P20742 TRUE _EEGTDLEVTANR_ _EEGTDLEVTANR_ 667.3151454 0.000139519 230759.89 noloss 7 y 1 802.4417428 79.06382 FALSE sp P20742 P20742 PZP_HUMAN Pregnancy zone protein Homo sapiens 9606 PZP 1 4 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _EEGTDLEVTANR_ -40 TRUE _EEGTDLEVTANR_ EEGTDLEVTANR 5.3526073 0.94296074 5.3526073|3.901706 P20742 TRUE _EEGTDLEVTANR_ _EEGTDLEVTANR_ 667.3151454 0.000139519 230759.89 noloss 8 y 1 917.4686859 72.09271 FALSE sp P20742 P20742 PZP_HUMAN Pregnancy zone protein Homo sapiens 9606 PZP 1 4 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _EEGTDLEVTANR_ -40 TRUE _EEGTDLEVTANR_ EEGTDLEVTANR 5.3526073 0.94296074 5.3526073|3.901706 P20742 TRUE _EEGTDLEVTANR_ _EEGTDLEVTANR_ 667.3151454 0.000139519 230759.89 noloss 9 y 1 1018.516364 21.396385 TRUE sp P20742 P20742 PZP_HUMAN Pregnancy zone protein Homo sapiens 9606 PZP 1 4 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _EEGTDLEVTANR_ -40 TRUE _EEGTDLEVTANR_ EEGTDLEVTANR 5.3526073 0.94296074 5.3526073|3.901706 P20742 TRUE _EEGTDLEVTANR_ _EEGTDLEVTANR_ 667.3151454 0.000139519 230759.89 noloss 10 y 1 1075.537828 83.90465 FALSE sp P20742 P20742 PZP_HUMAN Pregnancy zone protein Homo sapiens 9606 PZP 1 4 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _EEGTDLEVTANR_ -40 TRUE _EEGTDLEVTANR_ EEGTDLEVTANR 5.3526073 0.94296074 5.3526073|3.901706 P20742 TRUE _EEGTDLEVTANR_ _EEGTDLEVTANR_ 667.3151454 0.000139519 230759.89 H2O 6 y 1 671.3471141 8.983159 TRUE sp P20742 P20742 PZP_HUMAN Pregnancy zone protein Homo sapiens 9606 PZP 1 4 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 noloss 3 b 1 419.1231111 14.944622 TRUE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 noloss 3 y 1 436.1972791 30.738253 FALSE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 noloss 4 b 1 534.1500542 9.713619 TRUE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 noloss 4 y 1 583.2656931 51.723152 FALSE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 noloss 5 y 1 712.3082861 50.78903 FALSE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 noloss 6 y 1 841.3508792 59.771255 FALSE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 noloss 7 y 1 956.3778223 75.695114 FALSE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 noloss 8 y 1 1085.420415 100 FALSE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 noloss 9 y 1 1214.463008 15.559877 TRUE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 H2O 3 b 1 401.1125463 9.39616 TRUE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 H2O 4 b 1 516.1394894 5.2136855 TRUE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 NH3 4 y 1 566.2391447 6.1200476 TRUE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 H2O 5 y 1 694.2977213 6.602107 TRUE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 H2O 6 y 1 823.3403144 10.601803 TRUE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 H2O 7 y 1 938.3672575 6.748549 TRUE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 H2O 8 y 1 1067.409851 26.568663 TRUE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _C[+57]EEDEEFTC[+57]R_ -40 TRUE _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ CEEDEEFTCR -1.2823446 0.9011946 -1.2823446|-4.0177083 P00747 TRUE _C[+57]EEDEEFTC[+57]R_ _C[Carbamidomethyl (C)]EEDEEFTC[Carbamidomethyl (C)]R_ 687.7504667 0.00036315 385101.16 H2O 9 y 1 1196.452444 10.719879 TRUE sp P00747 P00747 PLMN_HUMAN Plasminogen Homo sapiens 9606 PLG 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 3 b 1 386.2034101 7.7662497 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 3 y 1 347.2037444 3.2926106 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 4 b 1 499.2874741 6.734219 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 4 y 1 475.2623219 14.221682 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 5 b 1 586.3195025 1.5547751 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 5 y 1 604.304915 12.158777 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 6 b 1 715.3620955 3.230758 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 6 y 1 675.3420288 25.758886 FALSE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 7 b 1 786.3992093 1.9753934 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 7 y 1 804.3846219 22.087849 FALSE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 8 b 1 915.4418024 1.8401791 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 8 b 2 458.2245394 1.6086894 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 8 y 1 891.4166503 74.71736 FALSE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 9 y 1 1004.500714 54.28254 FALSE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 10 b 1 1114.537494 1.0495659 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 10 y 1 1133.543307 100 FALSE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 11 y 1 1261.601885 24.588951 FALSE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 noloss 11 y 2 631.3045807 2.1570513 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 H2O 3 b 1 368.1928453 3.4925315 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 NH3 3 b 1 369.1768617 2.9452903 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 H2O 4 b 1 481.2769092 1.0290943 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 NH3 4 y 1 458.2357735 1.8126523 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 H2O 8 y 1 873.4060855 2.0101676 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 H2O 10 y 1 1115.532743 6.641937 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 H2O 11 y 2 622.2992983 6.5424037 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 H2O 11 y 1 1243.59132 3.3419182 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 NH3 11 y 1 1244.575336 10.56645 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 NH3 4 b 1 482.2609257 1.1637812 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 -IK_221028_C19_lib2_01 2 _KQELSEAEQATR_ -40 TRUE _KQELSEAEQATR_ KQELSEAEQATR -26.474043 0.9663669 -26.300653|-26.58661 P01024 TRUE _KQELSEAEQATR_ _KQELSEAEQATR_ 695.3520622 0.000291637 1674753 NH3 3 y 1 330.177196 1.6216956 TRUE sp P01024 P01024 CO3_HUMAN Complement C3 Homo sapiens 9606 C3 1 2 H_sapiens_uniprot_reviewed_cannonical_3AUP000005640_2-2022.08.12-15.33.51.77 diff --git a/implementations/python/tests/test_data/phl004_canonical_sall_pv_plasma.head.diann.tsv b/implementations/python/tests/test_data/phl004_canonical_sall_pv_plasma.head.diann.tsv deleted file mode 100644 index ea42718..0000000 --- a/implementations/python/tests/test_data/phl004_canonical_sall_pv_plasma.head.diann.tsv +++ /dev/null @@ -1,147 +0,0 @@ -FileName PrecursorMz ProductMz Tr_recalibrated IonMobility transition_name LibraryIntensity transition_group_id decoy PeptideSequence Proteotypic QValue PGQValue Ms1ProfileCorr ProteinGroup ProteinName Genes FullUniModPeptideName ModifiedPeptide PrecursorCharge PeptideGroupLabel UniprotID NTerm CTerm FragmentType FragmentCharge FragmentSeriesNumber FragmentLossType ExcludeFromAssay -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 778.41296 427.22995 117.9 0 AAAAAAAAAAAAAAAASAGGK2_98_1_0_6 1 AAAAAAAAAAAAAAAASAGGK2 0 AAAAAAAAAAAAAAAASAGGK 1 0 0 0 P0CG40 SP9_HUMAN SP9 AAAAAAAAAAAAAAAASAGGK AAAAAAAAAAAAAAAASAGGK 2 AAAAAAAAAAAAAAAASAGGK P0CG40 0 0 b 1 6 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 778.41296 498.26706 117.9 0 AAAAAAAAAAAAAAAASAGGK2_98_1_0_7 0.88039231 AAAAAAAAAAAAAAAASAGGK2 0 AAAAAAAAAAAAAAAASAGGK 1 0 0 0 P0CG40 SP9_HUMAN SP9 AAAAAAAAAAAAAAAASAGGK AAAAAAAAAAAAAAAASAGGK 2 AAAAAAAAAAAAAAAASAGGK P0CG40 0 0 b 1 7 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 778.41296 569.3042 117.9 0 AAAAAAAAAAAAAAAASAGGK2_98_1_0_8 0.66275221 AAAAAAAAAAAAAAAASAGGK2 0 AAAAAAAAAAAAAAAASAGGK 1 0 0 0 P0CG40 SP9_HUMAN SP9 AAAAAAAAAAAAAAAASAGGK AAAAAAAAAAAAAAAASAGGK 2 AAAAAAAAAAAAAAAASAGGK P0CG40 0 0 b 1 8 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 778.41296 356.19284 117.9 0 AAAAAAAAAAAAAAAASAGGK2_98_1_0_5 0.58039355 AAAAAAAAAAAAAAAASAGGK2 0 AAAAAAAAAAAAAAAASAGGK 1 0 0 0 P0CG40 SP9_HUMAN SP9 AAAAAAAAAAAAAAAASAGGK AAAAAAAAAAAAAAAASAGGK 2 AAAAAAAAAAAAAAAASAGGK P0CG40 0 0 b 1 5 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 778.41296 640.34131 117.9 0 AAAAAAAAAAAAAAAASAGGK2_98_1_0_9 0.44118175 AAAAAAAAAAAAAAAASAGGK2 0 AAAAAAAAAAAAAAAASAGGK 1 0 0 0 P0CG40 SP9_HUMAN SP9 AAAAAAAAAAAAAAAASAGGK AAAAAAAAAAAAAAAASAGGK 2 AAAAAAAAAAAAAAAASAGGK P0CG40 0 0 b 1 9 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 778.41296 703.37335 117.9 0 AAAAAAAAAAAAAAAASAGGK2_121_1_0_12 0.40000239 AAAAAAAAAAAAAAAASAGGK2 0 AAAAAAAAAAAAAAAASAGGK 1 0 0 0 P0CG40 SP9_HUMAN SP9 AAAAAAAAAAAAAAAASAGGK AAAAAAAAAAAAAAAASAGGK 2 AAAAAAAAAAAAAAAASAGGK P0CG40 0 0 y 1 9 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 778.41296 916.48468 117.9 0 AAAAAAAAAAAAAAAASAGGK2_121_1_0_9 0.40000239 AAAAAAAAAAAAAAAASAGGK2 0 AAAAAAAAAAAAAAAASAGGK 1 0 0 0 P0CG40 SP9_HUMAN SP9 AAAAAAAAAAAAAAAASAGGK AAAAAAAAAAAAAAAASAGGK 2 AAAAAAAAAAAAAAAASAGGK P0CG40 0 0 y 1 12 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 778.41296 1129.5961 117.9 0 AAAAAAAAAAAAAAAASAGGK2_121_1_0_6 0.36078224 AAAAAAAAAAAAAAAASAGGK2 0 AAAAAAAAAAAAAAAASAGGK 1 0 0 0 P0CG40 SP9_HUMAN SP9 AAAAAAAAAAAAAAAASAGGK AAAAAAAAAAAAAAAASAGGK 2 AAAAAAAAAAAAAAAASAGGK P0CG40 0 0 y 1 15 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 778.41296 774.41046 117.9 0 AAAAAAAAAAAAAAAASAGGK2_121_1_0_11 0.34117815 AAAAAAAAAAAAAAAASAGGK2 0 AAAAAAAAAAAAAAAASAGGK 1 0 0 0 P0CG40 SP9_HUMAN SP9 AAAAAAAAAAAAAAAASAGGK AAAAAAAAAAAAAAAASAGGK 2 AAAAAAAAAAAAAAAASAGGK P0CG40 0 0 y 1 10 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 778.41296 845.44757 117.9 0 AAAAAAAAAAAAAAAASAGGK2_121_1_0_10 0.30195799 AAAAAAAAAAAAAAAASAGGK2 0 AAAAAAAAAAAAAAAASAGGK 1 0 0 0 P0CG40 SP9_HUMAN SP9 AAAAAAAAAAAAAAAASAGGK AAAAAAAAAAAAAAAASAGGK 2 AAAAAAAAAAAAAAAASAGGK P0CG40 0 0 y 1 11 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 778.41296 490.26199 117.9 0 AAAAAAAAAAAAAAAASAGGK2_121_1_0_15 0.301357 AAAAAAAAAAAAAAAASAGGK2 0 AAAAAAAAAAAAAAAASAGGK 1 0 0 0 P0CG40 SP9_HUMAN SP9 AAAAAAAAAAAAAAAASAGGK AAAAAAAAAAAAAAAASAGGK 2 AAAAAAAAAAAAAAAASAGGK P0CG40 0 0 y 1 6 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 778.41296 419.22488 117.9 0 AAAAAAAAAAAAAAAASAGGK2_121_1_0_16 0.29999879 AAAAAAAAAAAAAAAASAGGK2 0 AAAAAAAAAAAAAAAASAGGK 1 0 0 0 P0CG40 SP9_HUMAN SP9 AAAAAAAAAAAAAAAASAGGK AAAAAAAAAAAAAAAASAGGK 2 AAAAAAAAAAAAAAAASAGGK P0CG40 0 0 y 1 5 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 778.41296 1058.5588 117.9 0 AAAAAAAAAAAAAAAASAGGK2_121_1_0_7 0.25881943 AAAAAAAAAAAAAAAASAGGK2 0 AAAAAAAAAAAAAAAASAGGK 1 0 0 0 P0CG40 SP9_HUMAN SP9 AAAAAAAAAAAAAAAASAGGK AAAAAAAAAAAAAAAASAGGK 2 AAAAAAAAAAAAAAAASAGGK P0CG40 0 0 y 1 14 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 778.41296 632.33624 117.9 0 AAAAAAAAAAAAAAAASAGGK2_121_1_0_13 0.2572208 AAAAAAAAAAAAAAAASAGGK2 0 AAAAAAAAAAAAAAAASAGGK 1 0 0 0 P0CG40 SP9_HUMAN SP9 AAAAAAAAAAAAAAAASAGGK AAAAAAAAAAAAAAAASAGGK 2 AAAAAAAAAAAAAAAASAGGK P0CG40 0 0 y 1 8 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 778.41296 853.45264 117.9 0 AAAAAAAAAAAAAAAASAGGK2_98_1_0_12 0.18174933 AAAAAAAAAAAAAAAASAGGK2 0 AAAAAAAAAAAAAAAASAGGK 1 0 0 0 P0CG40 SP9_HUMAN SP9 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AAAAAAAAAASGAAIPPLIPPR2_121_1_0_6 0.055300001 AAAAAAAAAASGAAIPPLIPPR2 0 AAAAAAAAAASGAAIPPLIPPR 1 0 0 0 O14654 IRS4_HUMAN IRS4 AAAAAAAAAASGAAIPPLIPPR AAAAAAAAAASGAAIPPLIPPR 2 AAAAAAAAAASGAAIPPLIPPR O14654 0 0 y 1 16 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 950.04419 692.44537 132.2 0 AAAAAAAAAASGAAIPPLIPPR2_121_1_0_16 0.044360001 AAAAAAAAAASGAAIPPLIPPR2 0 AAAAAAAAAASGAAIPPLIPPR 1 0 0 0 O14654 IRS4_HUMAN IRS4 AAAAAAAAAASGAAIPPLIPPR AAAAAAAAAASGAAIPPLIPPR 2 AAAAAAAAAASGAAIPPLIPPR O14654 0 0 y 1 6 noloss False -/home/andrew/hc-storage/diabetes_study/speclib/phl004_canonical_sall_pv.csv 950.04419 1543.8955 132.2 0 AAAAAAAAAASGAAIPPLIPPR2_121_1_0_5 0.036620002 AAAAAAAAAASGAAIPPLIPPR2 0 AAAAAAAAAASGAAIPPLIPPR 1 0 0 0 O14654 IRS4_HUMAN IRS4 AAAAAAAAAASGAAIPPLIPPR AAAAAAAAAASGAAIPPLIPPR 2 AAAAAAAAAASGAAIPPLIPPR O14654 0 0 y 1 17 noloss False diff --git a/implementations/python/tests/test_index.py b/implementations/python/tests/test_index.py deleted file mode 100644 index a10459b..0000000 --- a/implementations/python/tests/test_index.py +++ /dev/null @@ -1,47 +0,0 @@ -import os -import unittest -import tempfile - -from mzlib.backends import TextSpectralLibrary -from mzlib.index import MemoryIndex, SQLIndex - -from .common import datafile - -class IndexBehaviorBase(object): - test_file = datafile("chinese_hamster_hcd_selected_head.mzlb.txt") - index_cls = None - - def make_dir(self): - dirname = tempfile.mkdtemp("_test", "mzlb_") - return dirname - - def _open(self): - return TextSpectralLibrary(self.test_file) - - def _make_index(self, library): - library.index = self.index_cls() - library.create_index() - return library.index - - def test_sequence_behavior(self): - lib = self._open() - index = self._make_index(lib) - assert len(index) == 7 - record = index[3] - assert record.number == 4 - assert record.name == "AAAAGSTSVKPIFSR/2_0_44eV" - - -class TestMemoryIndex(unittest.TestCase, IndexBehaviorBase): - index_cls = MemoryIndex - - -class TestSQLIndex(unittest.TestCase, IndexBehaviorBase): - index_cls = SQLIndex - - def _make_index(self, library): - dirname = self.make_dir() - index_root = os.path.join(dirname, os.path.basename(self.test_file)) - library.index = self.index_cls(index_root) - library.create_index() - return library.index diff --git a/implementations/python/tests/test_library.py b/implementations/python/tests/test_library.py deleted file mode 100644 index 26614bb..0000000 --- a/implementations/python/tests/test_library.py +++ /dev/null @@ -1,17 +0,0 @@ -import os -import unittest -import tempfile - -from mzlib.spectrum_library import SpectrumLibrary - -from .common import datafile -from .test_library_backend import LibraryBehaviorBase - - -class TestSpectrumLibrary(unittest.TestCase, LibraryBehaviorBase): - library_cls = SpectrumLibrary - test_file = datafile("chinese_hamster_hcd_selected_head.mzlb.txt") - - def _open_library(self): - lib = self.library_cls(filename=self.test_file) - return lib diff --git a/implementations/python/tests/test_library_backend.py b/implementations/python/tests/test_library_backend.py deleted file mode 100644 index 1983002..0000000 --- a/implementations/python/tests/test_library_backend.py +++ /dev/null @@ -1,98 +0,0 @@ -import math -import os -import unittest - -from mzlib.spectrum import Spectrum -from mzlib.backends import (MSPSpectralLibrary, TextSpectralLibrary, JSONSpectralLibrary, SpectronautTSVSpectralLibrary, DIANNTSVSpectralLibrary) -from mzlib.analyte import ANALYTE_MIXTURE_TERM - -from .common import datafile - - -class LibraryBehaviorBase(object): - - def _open_library(self, file_path=None): - if file_path is None: - file_path = self.test_file - lib = self.library_cls(file_path) - return lib - - def test_sequence_behavior(self): - lib = self._open_library() - assert len(lib) == 7 - spec = lib[3] - assert spec.get_attribute( - "MS:1003061|library spectrum name") == "AAAAGSTSVKPIFSR/2_0_44eV" - - # TODO: Fix clipping in _buffer_from_stream first - def test_iteration(self): - lib = self._open_library() - assert list(lib) == list(lib.read()) - - -class TestMSPLibrary(unittest.TestCase, LibraryBehaviorBase): - test_file = datafile("chinese_hamster_hcd_selected_head.msp") - library_cls = MSPSpectralLibrary - - -class MzSpecLibLibraryBehaviorBase(LibraryBehaviorBase): - def test_interpretation_attribute(self): - try: - path = self.test_interpretation_file - except AttributeError: - return - lib = self._open_library(path) - spec: Spectrum = lib[0] - interp = spec.interpretations[1] - assert len(interp.attributes) == 2 - assert interp.get_attribute('MS:1002357|PSM-level probability') == 0.974 - assert interp.get_attribute(ANALYTE_MIXTURE_TERM) == [1, 2] - mem = interp.get_member_interpretation(1) - assert len(mem) == 1 - assert mem.get_attribute('MS:XXXXXXX|explained intensity fraction') == 0.287 - - -class TestTextLibrary(unittest.TestCase, MzSpecLibLibraryBehaviorBase): - test_file = datafile("chinese_hamster_hcd_selected_head.mzlb.txt") - library_cls = TextSpectralLibrary - test_interpretation_file = datafile("complex_interpretations_with_members.mzlb.txt") - - -class TestJSONLibrary(unittest.TestCase, MzSpecLibLibraryBehaviorBase): - test_file = datafile("chinese_hamster_hcd_selected_head.mzlb.json") - library_cls = JSONSpectralLibrary - test_interpretation_file = datafile("complex_interpretations_with_members.mzlb.json") - - -class TestSpectronautLibrary(unittest.TestCase, LibraryBehaviorBase): - test_file = datafile("human_serum.head.spectronaut.tsv") - library_cls = SpectronautTSVSpectralLibrary - - def test_sequence_behavior(self): - lib = self._open_library() - assert len(lib) == 9 - - spec: Spectrum = lib[0] - assert spec.name == 'AQIPILR/2' - assert math.isclose(spec.precursor_mz, 405.7634379) - assert spec.precursor_charge == 2 - - spec = lib[5] - assert spec.name == 'QELSEAEQATR/2' - assert math.isclose(spec.precursor_mz, 631.3045807) - assert spec.get_analyte(1).proteins[0].name == 'CO3_HUMAN' - - -class TestDIANNTSVLibrary(unittest.TestCase, LibraryBehaviorBase): - test_file = datafile("phl004_canonical_sall_pv_plasma.head.diann.tsv") - library_cls = DIANNTSVSpectralLibrary - - def test_sequence_behavior(self): - lib = self._open_library() - assert len(lib) == 9 - - spec: Spectrum = lib[0] - analyte = spec.get_analyte(1) - assert analyte.peptide == 'AAAAAAAAAAAAAAAASAGGK' - assert spec.name == 'AAAAAAAAAAAAAAAASAGGK2' - diff --git a/implementations/python/tests/test_msp_attributes.py b/implementations/python/tests/test_msp_attributes.py deleted file mode 100644 index 6b47b2a..0000000 --- a/implementations/python/tests/test_msp_attributes.py +++ /dev/null @@ -1,16 +0,0 @@ -import unittest - -from mzlib.backends import (MSPSpectralLibrary) -from mzlib.backends import msp - -from .common import datafile - - -class TestMSPAttributeConversion(unittest.TestCase): - def test_hierarchy(self): - flat_maps = (msp.analyte_terms, msp.other_terms, msp.interpretation_terms, msp.interpretation_member_terms) - handler_maps = (msp.msp_analyte_attribute_handler, msp.msp_spectrum_attribute_handler) - for handler_map in handler_maps: - for key in handler_map.mapping: - for flat_map in flat_maps: - assert key not in flat_map diff --git a/implementations/python/tests/test_spectrum.py b/implementations/python/tests/test_spectrum.py deleted file mode 100644 index 534486a..0000000 --- a/implementations/python/tests/test_spectrum.py +++ /dev/null @@ -1,32 +0,0 @@ -import os -import unittest -import tempfile - -from mzlib.backends import MSPSpectralLibrary, TextSpectralLibrary - -from .common import datafile - - -class TestSpectrum(unittest.TestCase): - - def get_library(self): - test_file = datafile("chinese_hamster_hcd_selected_head.mzlb.txt") - return TextSpectralLibrary(test_file) - - def get_spectrum(self, index): - library = self.get_library() - return library.get_spectrum(index) - - def test_write(self): - spectrum = self.get_spectrum(1) - buffer = spectrum.write('text') - lines = buffer.splitlines() - n_lines = len(lines) - assert n_lines == 131 - assert buffer.startswith("\nMS:1003061|library spectrum name") - - def test_equality(self): - spectrum = self.get_spectrum(1) - spectrum2 = self.get_spectrum(1) - assert spectrum == spectrum2 - diff --git a/implementations/python/tests/test_validate.py b/implementations/python/tests/test_validate.py deleted file mode 100644 index 1a71fc9..0000000 --- a/implementations/python/tests/test_validate.py +++ /dev/null @@ -1,39 +0,0 @@ -import unittest - -from mzlib.spectrum_library import SpectrumLibrary -from mzlib.validate import validator - -from .common import datafile - - -class TestLibrarySemanticValidator(unittest.TestCase): - def open_library(self): - test_file = datafile("chinese_hamster_hcd_selected_head.mzlb.txt") - library = SpectrumLibrary(filename=test_file) - return library - - def validate_library(self, valid): - library = self.open_library() - return valid.validate_library(library) - - def test_validate_base(self): - valid = validator.get_validator_for("base") - assert self.validate_library(valid) - - def test_validate_peptide(self): - valid = validator.get_validator_for("base") - valid = valid.chain(validator.get_validator_for("peptide")) - assert self.validate_library(valid) - - def test_validate_silver(self): - valid = validator.get_validator_for("base") - valid = valid.chain(validator.get_validator_for("silver")) - assert not self.validate_library(valid) - - def test_validate_peak_annotations(self): - valid = validator.get_validator_for("base") | validator.get_object_validator_for("peak_annotations") - assert self.validate_library(valid) - - test_file = datafile("bad_peak_annotations.mzlb.txt") - library = SpectrumLibrary(filename=test_file) - assert not valid.validate_library(library)