Hi guys, I've been putting some data through OMSSA and running it through Xinteract with a decoy database generated with the TPP reverse FASTA tool. Never had a problem before but in one of my latest data sets there remains about 50 decoy proteins in the prot.xml file out of a total of about 3000 protein hits, with quite high probability.
The names all indicate that they indeed do contain the decoy tag so I'm baffled, peptide prophet proceeds without any incident at all. Any suggestions as what to do or how to interpet this result in terms of peptide prophet models is appreciated. Has the TPP4.4 release changed the way TPP handles decoy hits? -- 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.
