Hi, I believe I've encountered a minor bug. After removing decoys using PeptideProphet, a peptide that belongs to both a decoy hit and a real hit will still have its decoy identifier as part of its list of possible proteins. That peptide can then become a one-hit wonder and the decoy identifier will be used as one of its possible identifiers. It would be nice if that decoy id was removed from the list of possible proteins. I've currently encountered the issue on 5 different runs (1 decoy protein with high probability was still in the ProteinProphet results for each). I'm using TPP 4.4.1 on Windows 7, human IPI database from 10/03/2010 semi-trypsin digest with full reverse decoy sequences (decoy protein identifiers prepended with "rev_"). I can send the original pep.xml files with the decoys for testing purposes.
-- Dennis Goldfarb Graduate Student Department of Computer Science University of North Carolina at Chapel Hill -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
