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).
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).