Hi Dennis, I don't think this is a bug, just a peculiarity of certain databases. It appears that you have some peptides that are common to both the target and decoy databases, this is generally a good think to avoid when generating the database since decoy hits are taken to be False Positives. I spectrum that hits a peptide present in both a the target and decoy sequences *cannot* be assumed as False Position (it must be given the benefit of the doubt). In my opinion, it is ok to leave the decoy in the list of hit proteins since the decoy of this sort will *always* belong to a larger group of proteins that includes at least one target protein. I think it should be of some value to know that your one-hit-wonder protein is identified by a peptide that also exists in the decoy database.
-David On Mon, Dec 13, 2010 at 2:42 PM, Dennis Goldfarb <[email protected]> wrote: > 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. > -- 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.
