Add hco3 adduct annotation method#673
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# Conflicts: # tests/Common/CommonStandardTests/Lipidomics/MsmsCharacterizationTests.cs
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Pull Request Overview
This PR adds support for HCO3- (bicarbonate) adduct annotation methods for various lipid classes in mass spectrometry analysis. The changes enable the identification and characterization of lipids when they form HCO3- adducts during negative ion mode analysis.
- Adds HCO3- adduct support to PC_d5, LPC_d5, and SM_d9 lipid characterization methods
- Implements comprehensive test coverage for HCO3- adduct annotation across multiple lipid classes (PC, LPC, Ether-PC, Ether-LPC, OxPC, Ether-OxPC, SM, and their variants)
- Extends existing lipid identification logic to handle the bicarbonate adduct ionization pattern
Reviewed Changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| tests/Common/CommonStandardTests/Lipidomics/MsmsCharacterizationTests.cs | Adds 9 new test methods covering HCO3- adduct annotation for ceramides, phosphocholines, lysophosphocholines, and sphingomyelins with various modifications (ether, oxidized, deuterated variants) |
| src/Common/CommonStandard/Lipidomics/MsmsCharacterization.cs | Implements HCO3- adduct handling logic in JudgeIfPhosphatidylcholineD5, JudgeIfLysopcD5, and JudgeIfSphingomyelinD9 methods with fragment ion detection and candidate molecule generation |
Comments suppressed due to low confidence (1)
tests/Common/CommonStandardTests/Lipidomics/MsmsCharacterizationTests.cs:2505
- The comment says "HexCer_NS test" but the test method is named "CerNsD7Test" and tests Ceramide d7 (Cer_d7), not HexCeramide (HexCer_NS). The comment should accurately describe what is being tested.
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| } | ||
| else if (adduct.AdductIonName == "[M+HCO3]-") | ||
| { | ||
| // //"[M-H]- -C3H9N" |
There was a problem hiding this comment.
The comment has an extra forward slash at the beginning. It should be // "[M-H]- -C3H9N" instead of // //"[M-H]- -C3H9N".
| } | ||
| else if (adduct.AdductIonName == "[M+HCO3]-") | ||
| { | ||
| // //"[M-H]- -C3H9N" |
There was a problem hiding this comment.
The comment has an extra forward slash at the beginning. It should be // "[M-H]- -C3H9N" instead of // //"[M-H]- -C3H9N".
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