Hi Ali,
Are you setting your instrument to collect only 2+ and 3+ data? Are you using the tandem bundled with TPP or the GPM version of tandem? Have you tried to process all your runs in one file? Thanks, -David On Wed, Oct 5, 2016 at 11:39 AM, Ali <sma.banijam...@gmail.com> wrote: > 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 <sma.ban...@gmail.com> 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 <sma.ban...@gmail.com> 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 <sma.ban...@gmail.com> 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 spctools-discu...@googlegroups.com. >>>>>>> To post to this group, send email to spctools...@googlegroups.com. >>>>>>> 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 spctools-discu...@googlegroups.com. >>>>> To post to this group, send email to spctools...@googlegroups.com. >>>>> 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 spctools-discu...@googlegroups.com. >>> To post to this group, send email to spctools...@googlegroups.com. >>> 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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > 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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