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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Spectral library generation writes dubious spectra #2279

Open Alexander-Sol opened 1 year ago

Alexander-Sol commented 1 year ago

Spectral library generation is writing all PSMs where the PEP is less than 0.5. (Hard-coded) This feels high, possibly a typo. @YulingDai, is this the intended behavior?

filteredPsmList = Parameters.AllPsms.Where(p => p.FdrInfo.PEP_QValue <= 0.01 || p.FdrInfo.PEP < 0.5).ToList();
                filteredPsmList.RemoveAll(b => b.IsDecoy);
                filteredPsmList.RemoveAll(b => b.IsContaminant);