Hello Rishika, In Ian's case back in 2008 as well as in your case today the search engine identified no correct peptide spectrum matches. Have you considered the data quality and the search parameters?
-David On Thu, Aug 15, 2013 at 2:03 PM, Joseph Slagel < [email protected]> wrote: > Rishika, > > Could you post the output you are seeing? Also please check your search > results. Often times if the search parameters are incorrect you won't get > enough good spectrum identifications for peptideprophet/proteinprophet. > > -Joe > > > > On Thu, Aug 15, 2013 at 1:55 PM, Rishika Bisaria > <[email protected]>wrote: > >> Hello Ian, >> even I am getting the same error, any clue regarding how to solve the >> problem will be really helpful. >> >> Regards, >> Rishika >> >> On Thursday, 13 November 2008 23:55:55 UTC-5, Ian wrote: >>> >>> Hi Natalie and Brain, >>> It seems I posted a half baked question. >>> >>> Here is a fresh TPP run and output, as you will see below Protein >>> prophet quits even when the peptide output probabilities are above >>> 0.05: >>> >>> [root@localhost output_added]# ../bin/xinteract -p0 -Noutput.xml -Op >>> pep.xml >>> >>> ../bin/xinteract (TPP v4.1 JETSTREAM rev 0, Build 200811111648 >>> (linux)) >>> >>> running: "/var/TPP_new/bin/**InteractParser 'output.xml' 'pep.xml' - >>> L'7'" >>> file 1: pep.xml >>> processed altogether 7850 results >>> >>> results written to file /var/TPP_new/output_added/**output.shtml >>> >>> command completed in 3 sec >>> >>> running: "/var/TPP_new/bin/**PeptideProphetParser 'output.xml' >>> MINPROB=0" >>> (X! Tandem (k-score)) (minprob 0) >>> init with X! Tandem (k-score) trypsin >>> MS Instrument info: Manufacturer: ThermoFinnigan, Model: LCQ Deca XP, >>> Ionization: ESI, Analyzer: Ion Trap, Detector: EMT >>> >>> PeptideProphet (TPP v4.1 JETSTREAM rev 0, Build 200811111648 (linux)) >>> AKeller@ISB >>> read in 504 1+, 3602 2+, 3610 3+, 0 4+, and 0 5+ spectra >>> Initialising statistical models ... >>> negmean = -0.551996 >>> negmean = -2.05583 >>> negmean = -1.56374 >>> negmean = -0.2 >>> negmean = -0.2 >>> Iterations: .........10.........20....... >>> model complete after 28 iterations >>> command completed in 3 sec >>> >>> running: "/var/TPP_new/bin/**ProphetModels.pl -i output.xml" >>> Analyzing output.xml ... >>> Parsing search results "/var/TPP_new/input_added/**7MIX_STD_110802_1 >>> (X! >>> Tandem (k-score))"... >>> => Total of 7716 hits. >>> Can't exec "gnuplot": No such file or directory at /var/TPP_new/bin/ >>> ProphetModels.pl line 376. >>> command completed in 0 sec >>> >>> running: "/var/TPP_new/bin/**DatabaseParser 'output.xml'" >>> command completed in 0 sec >>> >>> running: "/var/TPP_new/bin/**RefreshParser 'output.xml' '/var/TPP_new/ >>> fasta/crap.fasta.pro'" >>> - Building Commentz-Walter keyword tree... - Searching the tree... >>> - Linking duplicate entries... - Printing results... >>> >>> command completed in 2 sec >>> >>> running: "/var/TPP_new/cgi-bin/**PepXMLViewer.cgi -I /var/TPP_new/ >>> output_added/output.xml" >>> command completed in 2 sec >>> >>> running: "/var/TPP_new/bin/**ProteinProphet 'output.xml' >>> 'output.prot.xml' XML" >>> ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the >>> original Perl by A. Keller (TPP v4.1 JETSTREAM rev 0, Build >>> 200811111648 (linux)) >>> (xml input) (using degen pep info) >>> . . . reading in /var/TPP_new/output_added/**output.xml. . . >>> . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+ spectra with min prob 0.05 >>> no data - quitting >>> >>> Ian >>> >>> >>> Natalie Tasman wrote: >>> > Hello Ian, >>> > >>> > I'm not sure what's going on with ProteinProphet, but if you're >>> running >>> > xinteract on the commandline, you'll need to at least specify the >>> "-Op" >>> > option to run ProteinProphet as well. >>> > >>> > Natalie >>> > >>> > On Thu, Nov 13, 2008 at 8:57 AM, Ian <[email protected]> wrote: >>> > >>> > > >>> > > Hi All, >>> > > I am trying to give a dry run with TPP using the >>> > > "7MIX_STD_110802_1.xml' file available at >>> > > http://sashimi.sourceforge.**net/repository.html<http://sashimi.sourceforge.net/repository.html> >>> > > >>> > > All modules expect Protein Prophet work fine. It generates the >>> > > following error: >>> > > >>> > > C:\Inetpub\tpp-bin>**ProteinProphet.exe put2.xml outout >>> > > ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the >>> > > original Pe >>> > > rl by A. Keller (TPP v4.1 JETSTREAM rev 0, Build 200811101627 >>> (MinGW)) >>> > > (xml input) (using degen pep info) >>> > > . . . reading in C:/Inetpub/tpp-bin/put2.xml. . . >>> > > . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+ spectra with min prob >>> 0.05 >>> > > no data - quitting >>> > > >>> > > I have verified the peptide prophet output file put2.xml, it has a >>> > > number of hits with probability >0.05. >>> > > Any tips how to fix this issue? >>> > > >>> > > Also when I try running xinteract command, it does not invoke >>> Protein >>> > > Prophet ...stops after peptide prophet. I was able to generate these >>> > > errors on Fedora 8 also. >>> > > >>> > > Regards, >>> > > Ian >>> > > >>> > > > >>> > > >>> >> -- >> 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 http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- > 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 http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/groups/opt_out. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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