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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
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Kdn adding and diagnostic filtering #2383

Closed RayMSMS closed 3 months ago

RayMSMS commented 4 months ago
  1. Add Kdn sugar type in the dictionary
  2. Add a new function "DiagnosticIon filter", which uses the diagnostic ion to distinguish the isobaric peak. If we find 274/292 peak in Scan, we remove the glycan without A(NeuAc) in the candidate list.
  3. Add the corresponding test for the filter function. Isobaric case: H1N1A1 & N2K1.
codecov[bot] commented 4 months ago

Codecov Report

Attention: Patch coverage is 89.90536% with 32 lines in your changes missing coverage. Please review.

Project coverage is 93.69%. Comparing base (7dab370) to head (48267d9).

Files Patch % Lines
...yer/GlycoSearchTask/PostGlycoSearchAnalysisTask.cs 73.58% 3 Missing and 11 partials :warning:
...pheus/EngineLayer/GlycoSearch/GlycoSearchEngine.cs 86.79% 2 Missing and 5 partials :warning:
...Morpheus/EngineLayer/GlycoSearch/GlycanDatabase.cs 89.28% 1 Missing and 5 partials :warning:
...heus/EngineLayer/GlycoSearch/GlycoSpectralMatch.cs 92.30% 0 Missing and 2 partials :warning:
MetaMorpheus/EngineLayer/GlycoSearch/Glycan.cs 97.56% 0 Missing and 1 partial :warning:
...aMorpheus/EngineLayer/GlycoSearch/GlycoPeptides.cs 96.66% 1 Missing :warning:
...eus/EngineLayer/ModernSearch/ModernSearchEngine.cs 85.71% 1 Missing :warning:
Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2383/graphs/tree.svg?width=650&height=150&src=pr&token=m0HXyK8tFy&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2383?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) ```diff @@ Coverage Diff @@ ## master #2383 +/- ## ========================================== + Coverage 92.97% 93.69% +0.72% ========================================== Files 139 139 Lines 21668 21720 +52 Branches 2983 3004 +21 ========================================== + Hits 20146 20351 +205 + Misses 1043 910 -133 + Partials 479 459 -20 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2383?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [MetaMorpheus/EngineLayer/GlycoSearch/AdjNode.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2383?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FGlycoSearch%2FAdjNode.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL0Fkak5vZGUuY3M=) | `80.00% <ø> (ø)` | | | [MetaMorpheus/EngineLayer/GlycoSearch/GlycanBox.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2383?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FGlycoSearch%2FGlycanBox.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL0dseWNhbkJveC5jcw==) | `96.59% <100.00%> (+14.77%)` | :arrow_up: | | [...pheus/EngineLayer/GlycoSearch/LocalizationGraph.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2383?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FGlycoSearch%2FLocalizationGraph.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL0xvY2FsaXphdGlvbkdyYXBoLmNz) | `100.00% <100.00%> (ø)` | | | [MetaMorpheus/EngineLayer/GlycoSearch/ModBox.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2383?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FGlycoSearch%2FModBox.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL01vZEJveC5jcw==) | `90.90% <ø> (ø)` | | | [MetaMorpheus/EngineLayer/GlycoSearch/Node.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2383?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FGlycoSearch%2FNode.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL05vZGUuY3M=) | `88.00% <ø> (+21.33%)` | :arrow_up: | | [MetaMorpheus/EngineLayer/PsmTsv/PsmFromTsv.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2383?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FPsmTsv%2FPsmFromTsv.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1BzbVRzdi9Qc21Gcm9tVHN2LmNz) | `97.74% <100.00%> (+0.04%)` | :arrow_up: | | [...pheus/TaskLayer/GlycoSearchTask/GlycoSearchTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2383?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FGlycoSearchTask%2FGlycoSearchTask.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9HbHljb1NlYXJjaFRhc2svR2x5Y29TZWFyY2hUYXNrLmNz) | `97.59% <100.00%> (ø)` | | | [...rpheus/TaskLayer/GlycoSearchTask/WriteGlycoFile.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2383?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FGlycoSearchTask%2FWriteGlycoFile.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9HbHljb1NlYXJjaFRhc2svV3JpdGVHbHljb0ZpbGUuY3M=) | `95.18% <ø> (ø)` | | | [MetaMorpheus/EngineLayer/GlycoSearch/Glycan.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2383?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FGlycoSearch%2FGlycan.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL0dseWNhbi5jcw==) | `97.04% <97.56%> (+0.25%)` | :arrow_up: | | [...aMorpheus/EngineLayer/GlycoSearch/GlycoPeptides.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2383?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FGlycoSearch%2FGlycoPeptides.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL0dseWNvUGVwdGlkZXMuY3M=) | `88.39% <96.66%> (+0.35%)` | :arrow_up: | | ... and [5 more](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2383?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | | ... and [3 files with indirect coverage changes](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2383/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)