Hi I am using PeptideProphet on my X!Tandem search results. There are ~150 experiments and PeptideProphet works fine on most of them but for ~50 experiments, PeptideProphet returns zero probability for all of the peptides. Can some one please tell me what might be the issue?
*More Info:* I am using TPP v4.8 on Linux. PeptideProphet does not show an error when it produces zero probability for all of the search results. This is what I'm doing: -search with X!Tandem -Tandem2XML ./100.tandem.xml ./100.tandem.pep.xml -InteractParser ./100.interact.xml ./100.tandem.pep.xml -S -Etrypsin -PeptideProphetParser ./100.interact.xml ACCMASS PPM NOICAT MINPROB=0 Thank you very much, *Ali* -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
