PeptideProphet is doing it's job here by telling you that there is no distinct population of correct results in this search. I suspect your search parameters are the problem. This is orbitrap data so the charges should be known, but it seems Tandem only searched 2+ and 3+ for you, this is somewhat troubling. Tomorrow, I will check your parameters more carefully to try to identify the actual problem with your search.
-David On Tue, Oct 4, 2016 at 2:12 PM, Ali <[email protected]> wrote: > It appears that PeptideProphet fails, I am getting this message: > > using Accurate Mass Bins > using PPM mass difference > (X! Tandem) (minprob 0) > adding Accurate Mass mixture distr > init with X! Tandem trypsin > MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, > Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive > detector > > PeptideProphet (TPP v4.8.0 PHILAE, Build 201608051257-exported > (RedHatEnterpriseServer-x86_64)) AKeller@ISB > read in 0 1+, 14418 2+, 11080 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. > Initialising statistical models ... > negmean = 0.0533258 > negmean = 1 > negmean = 0.0376944 > negmean = -0.2 > negmean = -0.2 > negmean = -0.2 > negmean = -0.2 > Iterations: .........10.........20. > WARNING: Mixture model quality test failed for charge (2+). > WARNING: Mixture model quality test failed for charge (3+). > > 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]> 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. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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