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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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Only quantify peptides that clear the q-value threshold #2375

Open Alexander-Sol opened 2 weeks ago

Alexander-Sol commented 2 weeks ago

Previously, when we wrote the AllQuantifiedPeptides output, we filtered based off of PSM q-value. So you would have some peptides with high q-values reported in the quant results. This fixes that!

In order to fix that, I had to reconfigure FDR calculation at the PSM and Peptide level. I did this by adding two new fields to SpectralMatch: PsmFdrInfo and PeptideFdrInfo. The names are self explanatory. There are a variety of toggles that were added to specify when Psm level FDR info should be used and peptide level info should be used.

codecov[bot] commented 2 weeks ago

Codecov Report

Attention: Patch coverage is 96.94656% with 4 lines in your changes missing coverage. Please review.

Project coverage is 92.90%. Comparing base (9b3118c) to head (454d20c).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2375/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/2375?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 #2375 +/- ## ======================================= Coverage 92.89% 92.90% ======================================= Files 139 139 Lines 21435 21498 +63 Branches 2944 2952 +8 ======================================= + Hits 19913 19973 +60 - Misses 1043 1045 +2 - Partials 479 480 +1 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2375?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/PsmTsv/PsmTsvWriter.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2375?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FPsmTsv%2FPsmTsvWriter.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1BzbVRzdi9Qc21Uc3ZXcml0ZXIuY3M=) | `97.54% <100.00%> (ø)` | | | [MetaMorpheus/EngineLayer/SpectralMatch.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2375?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FSpectralMatch.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1NwZWN0cmFsTWF0Y2guY3M=) | `99.73% <100.00%> (+0.01%)` | :arrow_up: | | [MetaMorpheus/TaskLayer/MetaMorpheusTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2375?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FMetaMorpheusTask.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9NZXRhTW9ycGhldXNUYXNrLmNz) | `88.49% <100.00%> (ø)` | | | [...aMorpheus/TaskLayer/SearchTask/SearchParameters.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2375?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FSearchTask%2FSearchParameters.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9TZWFyY2hUYXNrL1NlYXJjaFBhcmFtZXRlcnMuY3M=) | `100.00% <100.00%> (ø)` | | | [...EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2375?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FFdrAnalysis%2FPEPValueAnalysisGeneric.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0ZkckFuYWx5c2lzL1BFUFZhbHVlQW5hbHlzaXNHZW5lcmljLmNz) | `95.72% <83.33%> (+<0.01%)` | :arrow_up: | | [...eus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2375?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FSearchTask%2FPostSearchAnalysisTask.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9TZWFyY2hUYXNrL1Bvc3RTZWFyY2hBbmFseXNpc1Rhc2suY3M=) | `93.42% <98.36%> (+0.16%)` | :arrow_up: | | [...pheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2375?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FFdrAnalysis%2FFdrAnalysisEngine.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0ZkckFuYWx5c2lzL0ZkckFuYWx5c2lzRW5naW5lLmNz) | `96.57% <90.90%> (+0.04%)` | :arrow_up: | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2375/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)