I highly recommend you start employing decoys in your search databases. I noticed you are not combining together the runs in the analysis. If the data was generated and searched in the same way it should be analysed together for better statistical power. I suggest you combine the results from all your runs and filter by the spectrum names later. Try this:
InteractParser ./ALL.interact.xml ./*.tandem.pep.xml -S -Etrypsin PeptideProphetParser ./ALL.interact.xml ACCMASS PPM NOICAT MINPROB=0 -David On Mon, Oct 3, 2016 at 2:39 PM, Ali <[email protected]> wrote: > Hi David > > Thanks for your reply. I don't think so, it is not just one set, as I said > almost a third of my search results are returned with zero probabilities. > All of the searches are done with the same setting and using the same > database. The fact that for some of the searched files I am getting zero > probabilities and some of them are just fine is a bit strange. I don't have > decoys in my data base. If it helps, I can send you one of the search > results with or without PeptideProphet probabilities. > > Sincerely, > Ali > > > > On Monday, October 3, 2016 at 4:19:05 PM UTC-4, David Shteynberg wrote: >> >> Is it possible there are no correct results in that set? Common pitfalls >> are incorrect search parameters (e.g. wrong mods enabled or disabled) and >> wrong database. If you have decoys in your database these can be utilized >> for a more accurate mixture model generation using options "DECOY=<your >> decoy prefix> DECOYPROBS NONPARAM" in additions to the options you already >> have enabled. >> >> -David >> >> On Mon, Oct 3, 2016 at 10:39 AM, Ali <[email protected]> wrote: >> >>> 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. >>> >> >> -- > 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. > -- 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.
