Peptide Level PEP-Q Value changes #2431
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #2431 +/- ##
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Coverage 93.73% 93.73%
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Files 141 141
Lines 21871 21873 +2
Branches 2998 2998
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+ Hits 20500 20502 +2
Misses 922 922
Partials 449 449
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nbollis
reviewed
Oct 28, 2024
nbollis
approved these changes
Oct 29, 2024
trishorts
approved these changes
Oct 30, 2024
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This PR changes the way PSMs are rolled up to peptides for the purpose of PEP-Q Value calculations.
When calculating PEPQ Values at the peptide level, you first have to select the a PSM to represent each full sequence (peptide/proteoform). Previously, PSMs were selected based on their MetaMorpheus score. Now, PSMs will be selected based on PEP (lowest PEP PSM represents the full sequence, MetaMorpheus score is used as a tie-breaker).
The AllPeptides/AllProteoforms outputs will change as a result of this PR. The PSM with the lowest PEP will be used to represent each peptides. The output will still be ordered by MetaMorpheus score. All entries will have a PEP-Q value <= 1.