Thank you very much! I really appreciate it! On Tuesday, October 4, 2016 at 8:03:27 PM UTC-4, David Shteynberg wrote: > > 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] <javascript:>> > 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] <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. >> > >
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