Hi Kelly, I noticed PeptideProphet reads in 4+, 5+ and 6+ but no 2+ or 3+ peptides. This seems unusual. There are also more decoy hits than non-decoys, which isn't what you (or PeptideProphet) want. Is this what you see in the Comet results?
Cheers, Magnus On Monday, 11 March 2019 17:48:12 UTC+1, Kelly Rios wrote: > > Hi all, > > I have been getting an error when using Peptide Prophet under the Comet > pipeline. > > The comet search itself runs fine and the pep.xml output file from the > comet search looks good (many spectra listed). When I go to analyze the > peptides in peptide prophet, I get an error that the output file cannot be > found (*file not found*: not created or deleted?) > > I have attached screenshots of what the input parameters are for the > peptide prophet page, and what the failed command error looks like. > > I have tried this now with several different input file types, but keep > getting this error. > > I have not had this error before when analyzing MS data in comet. > > Has anyone else seen this issue recently? I have done a quick search on > here myself, but none of the answers seemed to be relevant to this > particular issue. > > Please let me know, > > Kelly Rios > -- 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.
