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Changes to PEP Calculation and Filtering #2387

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merged 56 commits into from
Aug 5, 2024

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Alexander-Sol
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There have been several iterations of this guy, but all the tests are finally passing. See also PR 2376

Currently, the pep q-value is computed by summing the pep and dividing by row number for psms or peptides sorted in descending order by MetaMorpheus score.

In this PR, pep is used to re-score the psms/peptides. PSMs are sorted in ascending order (good to bad) and then pep q-value is computed from bottom to top like we recently did for q-value using the formula (cumulative decoy count + 1) / cumulative target count).

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Alexander-Sol commented Jul 29, 2024

image

These are the results from a search @trishorts ran using an arabidopsis entrapment database

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10/10

@trishorts trishorts merged commit 4e95528 into smith-chem-wisc:master Aug 5, 2024
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4 participants