10000 decoys in target PSMs file · Issue #288 · percolator/percolator · GitHub
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decoys in target PSMs file #288

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wsnoble opened this issue Feb 3, 2021 · 0 comments
Open

decoys in target PSMs file #288

wsnoble opened this issue Feb 3, 2021 · 0 comments

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@wsnoble
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wsnoble commented Feb 3, 2021

Some search engines (e.g., Comet) will allow the same peptide sequence to appear in both the target and decoy databases. when this happens, Percolator will happily report a PSM that includes both target and decoy protein IDs, even though the PSM appears in the "targets" output file. I think the decoys should not be reported in that file.

Here is the command line:

percolator --results-peptides crux-output/20150513_QEP2_FBU_AB_3D_set1_8h_03.percolator.target.peptides.txt --decoy-results-peptides crux-output/20150513_QEP2_FBU_AB_3D_set1_8h_03.percolator.decoy.peptides.txt --results-psms crux-output/20150513_QEP2_FBU_AB_3D_set1_8h_03.percolator.target.psms.txt --decoy-results-psms crux-output/20150513_QEP2_FBU_AB_3D_set1_8h_03.percolator.decoy.psms.txt --verbose 2 --protein-decoy-pattern decoy_ --seed 1 --subset-max-train 0 --trainFDR 0.01 --testFDR 0.01 --maxiter 10 --search-input concatenated --test-each-iteration --klammer --no-schema-validation --protein-enzyme trypsin --fido-protein --fido-empirical-protein-q --fido-gridsearch-depth 0 --fido-fast-gridsearch 0 --fido-protein-truncation-threshold 0.01 --fido-gridsearch-mse-threshold 0.05 --results-proteins crux-output/20150513_QEP2_FBU_AB_3D_set1_8h_03.percolator.target.proteins.txt --decoy-results-proteins crux-output/20150513_QEP2_FBU_AB_3D_set1_8h_03.percolator.decoy.proteins.txt --post-processing-tdc crux-output/20150513_QEP2_FBU_AB_3D_set1_8h_03.make-pin.pin

I can send you the pin file separately (too big to attach).
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