Thanks for your recommendations David. I added decoys to my data base and I am still getting 0 probabilities for all of the hits. I am attaching my X! Tandem search parameters xml, could you please kindly do me a big favor and check it to see if there is anything suspicious there which might cause the issue? I am using Trypsin enzyme and TMT 10 plex of K and TMT 10plex of N term fixed residue modification.
Sincerely, *Ali* On Monday, October 3, 2016 at 5:57:39 PM UTC-4, David Shteynberg wrote: > > 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] <javascript:>> > 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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.
input100.xml
Description: XML document
default_no_k.xml
Description: XML document
