Merge pull request #26 from hgb-bin-proteomics/develop

MS Annika 3.0.2

HISTORY.md

@@ -1,5 +1,16 @@
 # History
 
+## MS Annika 3.0 v3.0.2
+
+- Release date: 18. June 2024
+- Supported Proteome Discoverer versions: 3.1
+- Changes:
+  - Major:
+    - New search algorithm to support non-cleavable crosslinkers
+  - Minor:
+    - Accessions and positions of decoy peptides are now also reported
+    - Support for validation with [xiFDR](https://www.rappsilberlab.org/software/xifdr/) using the [xiFDR exporter](https://github.com/hgb-bin-proteomics/MSAnnika_exporters)
+
 ## MS Annika 2.0 v2.2.2
 
 - Release date: 17. October 2023

README.md

@@ -1,34 +1,42 @@
 # MS Annika
 
-MS Annika is a crosslink search engine based on [MS Amanda](https://dx.doi.org/10.1021/pr500202e), aimed at identifying crosslinks of MS2-cleavable crosslinkers from MS2 and MS3 spectra.
+MS Annika is a crosslink search engine based on [MS Amanda](https://dx.doi.org/10.1021/pr500202e), aimed at identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and MS3 spectra.
 
 You can read more about MS Annika [here](https://ms.imp.ac.at/?action=ms-annika), [here](https://doi.org/10.1021/acs.jproteome.0c01000) and [here](https://doi.org/10.1021/acs.jproteome.3c00325).
 
 **This repository contains the latest release versions of MS Annika.**
 
-- Latest MS Annika 2.0 [version](https://raw.githubusercontent.com/hgb-bin-proteomics/MSAnnika/master/releases/latest/PD3.1/version.txt) for Proteome Discoverer 3.1: [**download**](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.1/latest.zip)
+- Latest MS Annika 3.0 [version](https://raw.githubusercontent.com/hgb-bin-proteomics/MSAnnika/master/releases/latest/PD3.1/version.txt) for Proteome Discoverer 3.1: [**download**](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.1/latest.zip)
 - Latest MS Annika 2.0 [version](https://raw.githubusercontent.com/hgb-bin-proteomics/MSAnnika/master/releases/latest/PD3.0/version.txt) for Proteome Discoverer 3.0: [**download**](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.0/latest.zip)
 - Latest MS Annika 2.0 [version](https://raw.githubusercontent.com/hgb-bin-proteomics/MSAnnika/master/releases/latest/PD2.5/version.txt) for Proteome Discoverer 2.5: [**download**](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD2.5/latest.zip)
 - Latest MS Annika [version](https://raw.githubusercontent.com/hgb-bin-proteomics/MSAnnika/master/releases/latest/PD2.4/version.txt) for Proteome Discoverer 2.4: [**download**](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD2.4/latest.zip)
 - Latest MS Annika [version](https://raw.githubusercontent.com/hgb-bin-proteomics/MSAnnika/master/releases/latest/PD2.3/version.txt) for Proteome Discoverer 2.3: [**download**](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD2.3/latest.zip)
 
 A list of changes in every version can be found in [HISTORY.md](https://github.com/hgb-bin-proteomics/MSAnnika/blob/master/HISTORY.md).
 
+## Parameters & Results
+
+Please refer to the [MS Annika User Manual](https://github.com/hgb-bin-proteomics/MSAnnika/blob/master/MS_Annika_3.0_UserManual.pdf) for a detailed description of all MS Annika parameters as
+well as descriptions of all result tables. For further down-stream analysis of MS Annika results we recommend taking a look at [MS Annika Extensions](https://github.com/hgb-bin-proteomics/MSAnnika_Extensions).
+
 ## Tutorial
 
-A tutorial of how to use MS Annika 2.0 can be found here: [Text](https://github.com/hgb-bin-proteomics/MSAnnika/blob/master/tutorial/MS_Annika_2.0_Tutorial.pdf) / [Video](https://www.youtube.com/watch?v=L1lVt35PYv4)
+A tutorial of how to use MS Annika 3.0 can be found here: [Text](https://github.com/hgb-bin-proteomics/MSAnnika/blob/master/tutorial/MS_Annika_3.0_Tutorial.pdf) / [Video](https://www.youtube.com/watch?v=L1lVt35PYv4)
 
 ## Example Files
 
-Example files to try MS Annika 2.0 can either be downloaded from [PRIDE](https://www.ebi.ac.uk/pride/archive/projects/PXD041955) or directly here:
-- Minimal example for MS2 search: [MGF + fasta](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/examples/data.zip)
-- RAW file for MS3 search: [RAW](https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/08/PXD041955/20211219_Eclipse_LC4_G2_Trap_backflash_Peplib20_DSSO_pl1_MS3_OTOTOT.raw)
+Example files to try MS Annika 3.0 can either be downloaded from [PRIDE](https://www.ebi.ac.uk/pride/archive/projects/PXD041955) or directly here:
+- Minimal example for a cleavable crosslink MS2 search: [MGF + fasta](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/examples/data.zip)
+- RAW file for a non-cleavable crosslink MS2 search: [RAW](https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/07/PXD014337/XLpeplib_Beveridge_QEx-HFX_DSS_R1.raw)
+- RAW file for a cleavable crosslink MS3 search: [RAW](https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/08/PXD041955/20211219_Eclipse_LC4_G2_Trap_backflash_Peplib20_DSSO_pl1_MS3_OTOTOT.raw)
 
 ## Example Workflows
 
 Example workflows that can be used in Proteome Discoverer:
 
 - Proteome Discoverer 3.0 / 3.1:
+  - DSS/BS3 MS2 search (CID, ETD, HCD, stepped HCD): [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.1/DSS.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.1/DSS.zip)
+  - DSS/BS3 MS2 search (for large datasets and proteome-wide searches, CID, ETD, HCD, stepped HCD): [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.1/DSS_big.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.1/DSS_big.zip)
   - DSSO MS2 search (CID, ETD, HCD, stepped HCD): [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_MS2.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_MS2.zip)
   - DSSO MS2-MS3 search (MS3 recorded in the orbitrap): [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_MS2_MS3_Orbitrap.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_MS2_MS3_Orbitrap.zip)
   - DSSO MS2-MS3 search (MS3 recorded in the ion trap): [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_MS2_MS3_Iontrap.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_MS2_MS3_Iontrap.zip)
@@ -48,19 +56,30 @@ For MS2 searches (CID, ETD, HCD, stepped HCD) it can also be beneficial to emplo
 
 - DSSO MS2 search with IMP MS2 Spectrum Processor: [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_IMP_MS2.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_IMP_MS2.zip)
 
-This workflow additionally requires the installation of the [IMP MS2 Spectrum Processor](https://ms.imp.ac.at/?action=spectrum-processor) node beforehand, which can be directly downloaded from [here](https://ms.imp.ac.at/?file=spectrum-processor/ms2spectrumprocessor_3.0.zip).
+This workflow additionally requires the installation of the [IMP MS2 Spectrum Processor](https://ms.imp.ac.at/?action=spectrum-processor) node beforehand, which can be directly downloaded from [here (Proteome Discoverer 3.0)](https://ms.imp.ac.at/?file=spectrum-processor/ms2spectrumprocessor_3.0.zip).
 
 ## Support for MGF and timsTOF Data
 
 The following MS Annika versions support MGF\* and timsTOF\*\* data input:
-- Proteome Discoverer 3.1: [MS Annika 2.0 v2.2.1](https://github.com/hgb-bin-proteomics/MSAnnika/releases/tag/v2.2.1)
+- Proteome Discoverer 3.1: [MS Annika 2.0 v2.2.1](https://github.com/hgb-bin-proteomics/MSAnnika/releases/tag/v2.2.1) or greater (e.g. [**latest**](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.1/latest.zip))
 - Proteome Discoverer 3.0: [MS Annika 2.0 v1.1.4fix](https://github.com/hgb-bin-proteomics/MSAnnika/releases/tag/v1.1.4fix)
 - Proteome Discoverer <=2.5: [MS Annika 1.0 v1.0.0](https://github.com/hgb-bin-proteomics/MSAnnika/releases/tag/v1.0.0)\*\*\*
 
-\*MS Annika 2.0 only supports MS2 search for MGF files since MGF files don't contain sufficient MS3 information.  
-\*\*requires installation of the Bruker Ion Mobility reader.  
+\*MS Annika 3.0 only supports MS2 search for MGF files since MGF files don't contain sufficient MS3 information.  
+\*\*optionally requires installation of the Bruker Ion Mobility reader to display ion mobilities in Proteome Discoverer, the node is not needed for crosslink search.  
 \*\*\*requires installation of the [IMP MS2 Spectrum Processor](https://ms.imp.ac.at/?action=spectrum-processor) node.
 
+## Getting Help
+
+In case something isn't working or if you need any help with MS Annika or one of
+the MS Annika extensions, please don't hesitate to reach out to us. You can open
+up an issue [here](https://github.com/hgb-bin-proteomics/MSAnnika/issues) or
+start a discussion
+[there](https://github.com/hgb-bin-proteomics/MSAnnika/discussions).
+We are usually fast to respond on GitHub and other users might be able to help
+too! Alternatively, you can always drop us an email at the addresses
+[below](#contact).
+
 ## Known Issues
 
 [List of known issues](https://github.com/hgb-bin-proteomics/MSAnnika/issues)
@@ -85,3 +104,4 @@ DOI: 10.1021/acs.jproteome.0c01000
 ## Contact
 
 - [[email protected]](mailto:[email protected])
+- [[email protected]](mailto:[email protected])

prereleases/3.0.0/PD3.1/version.txt

@@ -0,0 +1 @@
+MS Annika 3.0 version 3.0.0 (pre-release)

prereleases/3.0.1/PD3.1/version.txt

@@ -0,0 +1 @@
+MS Annika 3.0 version 3.0.1 (pre-release)

prereleases/info.txt

@@ -0,0 +1,8 @@
+This directory contains pre-release versions of MS Annika. These versions are stable development versions, that might however still contain some bugs and are not yet optimized.
+These versions only come in the from of DLLs and without an installer. To install it, do the following steps:
+- First install one of the previous MS Annika versions for your Proteome Discoverer version.
+- Navigate to the installation directory of Proteome Discoverer:
+	- For example: C:/Program Files/Thermo/Proteome Discoverer 3.1/Proteome Discoverer 3.1/Thermo.Magellan.Server
+- Copy and paste all MS Annika DLLs into that folder.
+- Open a terminal in that folder and run "Thermo.Magellan.Server.exe -install".
+- Done!

releases/3.0.2/PD3.1/version.txt

@@ -0,0 +1 @@
+MS Annika 3.0 version 3.0.2

releases/latest/PD3.1/version.txt

@@ -1 +1 @@
-MS Annika 2.0 version 2.2.2
+MS Annika 3.0 version 3.0.2