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compomics / peptide-shaker-2.0-issue-tracker

Issue tracker for the beta release of PeptideShaker 2.0
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Proteins have less peptides than before #1

Closed hbarsnes closed 5 years ago

hbarsnes commented 5 years ago

Some proteins have a lot less peptides mapping to them than before. Example: P08238 (Heat shock protein HSP 90-beta (HS90B_HUMAN)) used to have 32 peptides, now it only has 10...

(Tested by loading only the X! Tandem identifications of the example dataset.)

dominik-kopczynski commented 5 years ago

Something goes terribly wrong, when I launch two times the same analysis with exactly the same SG result file and parameter file in PS, I get sometimes 9 peptides for P08238, sometimes 10 peptides.

hbarsnes commented 5 years ago

Is this still an issue? I cannot seem to reproduce it with the current code?