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Fix spectra export nist format (#449)
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* Revert "Fix DMEDFAHFA spectrumGenerator bug"

This reverts commit 28af6a1.

* Fix DMEDFAHFA spectrum generator

(cherry picked from commit e115c5d)

* no message

* 20230912

* MSDIAL v5.1.230918 release

* Merge branch 'master' into mikiko.takahashi

# Conflicts:
#	src/MSDIAL5/MsdialGuiApp/Properties/Resources.resx

* Fix OH counting in LipidmicsConverter

* Fix BisMeLPA annotation method

* Add Cer_ABP annotation method (CID-pos)

* Add CerABP annotation method (CID-neg)

* Add CerABP annotation method (EIEIO) WIP

* Fix CerABP annotation method (EIEIO)

* Fix CerABP annotation method (EIEIO)
Fix ShingoChainParser

* Add IONMODE

* no message

* Fix test

* local

* Change dll ver

* Change dll version

* Fix csproj

* Delete src/MSDIAL5/MsdialGuiApp/Properties/Resources.resx.rej

* Update MsdialCore.csproj

---------

Co-authored-by: mikiko.takahashi <[email protected]>
Co-authored-by: htsugawa <[email protected]>
Co-authored-by: YukiMatsuzawa <[email protected]>
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@mikikot113 @htsugawa @YukiMatsuzawa
4 people authored Nov 13, 2024
1 parent f636699 commit 4b50f40
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Showing 7 changed files with 11 additions and 4 deletions.
2 changes: 1 addition & 1 deletion src/MSDIAL4/ChromatogramUI/Chromatogram.csproj
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Expand Up @@ -38,8 +38,8 @@
<ProjectReference Include="..\..\Common\CommonMVVM\CommonMVVM.csproj" />
<ProjectReference Include="..\..\Common\CommonStandard\CommonStandard.csproj" />
<ProjectReference Include="..\DataProcessingStandard\DataProcessingStandard.csproj" />
<PackageReference Include="RawDataHandler" Version="1.0.*" Condition="'$(Configuration)'=='Debug'" />
<PackageReference Include="RawDataHandler" Version="1.0.*" Condition="'$(Configuration)'=='Release'" />
<PackageReference Include="RawDataHandler" Version="1.2.9013.327" Condition="'$(Configuration)'=='Debug'"/>
<PackageReference Include="RawDataHandler-Vendor-UnSupported" Version="1.0.*-*" Condition="'$(Configuration)'=='Debug vendor unsupported'" />
<PackageReference Include="RawDataHandler-Vendor-UnSupported" Version="1.0.*" Condition="'$(Configuration)'=='Release vendor unsupported'" />
<PackageReference Include="System.Data.SQLite.Core" Version="1.0.115.5" />
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2 changes: 1 addition & 1 deletion src/MSDIAL4/MsdialGcmsProcessStandard/MsdialGcmsProcessStandard.csproj
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Expand Up @@ -8,7 +8,7 @@

<ItemGroup>
<PackageReference Include="RawDataHandler" Version="1.0.*" Condition="'$(Configuration)'=='Release'" />
<PackageReference Include="RawDataHandler" Version="1.0.8763.372" Condition="'$(Configuration)'=='Debug'" />
<PackageReference Include="RawDataHandler" Version="1.2.9013.327" Condition="'$(Configuration)'=='Debug'"/>
<PackageReference Include="RawDataHandler-Vendor-UnSupported" Version="1.0.*-*" Condition="'$(Configuration)'=='Debug vendor unsupported'" />
<PackageReference Include="RawDataHandler-Vendor-UnSupported" Version="1.0.*" Condition="'$(Configuration)'=='Release vendor unsupported'" />
</ItemGroup>
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2 changes: 1 addition & 1 deletion src/MSDIAL4/MsdialLcmsProcessStandard/MsdialLcmsProcessStandard.csproj
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Expand Up @@ -8,7 +8,7 @@

<ItemGroup>
<PackageReference Include="RawDataHandler" Version="1.0.*" Condition="'$(Configuration)'=='Release'" />
<PackageReference Include="RawDataHandler" Version="1.0.8763.372" Condition="'$(Configuration)'=='Debug'" />
<PackageReference Include="RawDataHandler" Version="1.2.9013.327" Condition="'$(Configuration)'=='Debug'"/>
<PackageReference Include="RawDataHandler-Vendor-UnSupported" Version="1.0.*-*" Condition="'$(Configuration)'=='Debug vendor unsupported'" />
<PackageReference Include="RawDataHandler-Vendor-UnSupported" Version="1.0.*" Condition="'$(Configuration)'=='Release vendor unsupported'" />
</ItemGroup>
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2 changes: 2 additions & 0 deletions src/MSDIAL5/MsdialCore/Export/NistRecordBuilder.cs
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Expand Up @@ -14,6 +14,7 @@ public sealed class NistRecordBuilder
"NAME",
"PRECURSORMZ",
"PRECURSORTYPE",
"IONMODE",
"RETENTIONTIME",
"RETENTIONINDEX",
"MOBILITY",
Expand Down Expand Up @@ -152,6 +153,7 @@ public void SetComment(AlignmentSpotProperty spot) {

public void SetIonPropertyProperties(IIonProperty ionProperty) {
_contents["PRECURSORTYPE"] = ionProperty.AdductType.AdductIonName;
_contents["IONMODE"] = ionProperty.AdductType.IonMode.ToString();
_contents["CCS"] = ionProperty.CollisionCrossSection.ToString();
}

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2 changes: 1 addition & 1 deletion src/RawDataApp/RawDataConverter/RawDataConverter.csproj
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Expand Up @@ -13,7 +13,7 @@
</ItemGroup>
<ItemGroup>
<PackageReference Include="RawDataHandler" Version="1.0.*" Condition="'$(Configuration)'=='Release'" />
<PackageReference Include="RawDataHandler" Version="1.0.8763.372" Condition="'$(Configuration)'=='Debug'" />
<PackageReference Include="RawDataHandler" Version="1.2.9013.327" Condition="'$(Configuration)'=='Debug'" />
<PackageReference Include="RawDataHandler-Vendor-UnSupported" Version="1.0.*-*" Condition="'$(Configuration)'=='Debug vendor unsupported'" />
<PackageReference Include="RawDataHandler-Vendor-UnSupported" Version="1.0.*" Condition="'$(Configuration)'=='Release vendor unsupported'" />
</ItemGroup>
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2 changes: 2 additions & 0 deletions tests/MSDIAL5/MsdialCoreTests/Export/NistRecordBuilderTests.cs
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Expand Up @@ -77,6 +77,7 @@ public void Export_WritesExpectedNistFormat()
$@"NAME: TestCompound
PRECURSORMZ: 250.15
PRECURSORTYPE: [M+H]+
IONMODE: Positive
RETENTIONTIME: 5.5
FORMULA: C10H20
ONTOLOGY: Test Ontology
Expand Down Expand Up @@ -167,6 +168,7 @@ public void Export_WriteCCSProperty()
$@"NAME: Unknown|ID=1|MZ=250.15|RT=5.5|DT=6
PRECURSORMZ: 250.15
PRECURSORTYPE: [M+H]+
IONMODE: Positive
RETENTIONTIME: 5.5
MOBILITY: 6
CCS: 150.5
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3 changes: 3 additions & 0 deletions tests/MSDIAL5/MsdialCoreTests/Export/SpectraExportTests.cs
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Expand Up @@ -23,6 +23,7 @@ public void SaveSpectraTableAsNistFormatTest()
$@"NAME: XXX
PRECURSORMZ: 200
PRECURSORTYPE: [M+H]+
IONMODE: Positive
RETENTIONTIME: 3
FORMULA: C6
ONTOLOGY: Molecule ontology
Expand Down Expand Up @@ -108,6 +109,7 @@ public void SaveSpectraTableAsNistFormatUnknownTest()
$@"NAME: Unknown|ID=0|MZ=200|RT=3
PRECURSORMZ: 200
PRECURSORTYPE: [M+H]+
IONMODE: Positive
RETENTIONTIME: 3
FORMULA: C6
ONTOLOGY: Molecule ontology
Expand Down Expand Up @@ -189,6 +191,7 @@ public void SaveSpectraTableAsNistFormatGenericTest()
$@"NAME: TestCompound
PRECURSORMZ: 250.15
PRECURSORTYPE: [M+H]+
IONMODE: Positive
RETENTIONTIME: 5.5
FORMULA: C10H20
ONTOLOGY: Test Ontology
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