Many thanks Natalie, we'll take a detailed look at the spectra to check the quality. In the meantime we've explored PeptideProphet's command options on the data, and the RUN PeptideProphet command completes ok provided that "automatic mixture model checks" is bypassed and the wiff data was converted to mzXML by ProteoWizard. Under these same settings the command doesn't execute if mzWIFF (4.3.1) was used for the conversion - something we noticed was that there seems to be an issue with parsing the details of the mass spectrometer used. We'll generate an example of this error if it hasn't come up in other discussions and post it shortly,
Regards, Tabo On Oct 5, 10:50 pm, Natalie Tasman <[email protected]> wrote: > The relevant line is "=> Total of 0 hits." Take a look at the > interact.pep.xml file and see if there really are any results with>0.05 > probability values. It's possible that while the search did > > complete without error, the input comes from a bad sample, or the > search parameters may not be set correctly (wrong database used, etc). > > Natalie > > > > On Fri, Oct 2, 2009 at 12:29 AM, Tabo <[email protected]> wrote: > > > Hi there, > > we recently installed TPP (v4.3 JETSTREAM rev 1, Build 200909091257 > > (MinGW)) on a Windows XP (SP2 machine). The data we're analysing is > > generated on an ABI/SCIEX QStar, which we've converted into mzXML > > using mzwiff. > > > The mzXML data converts fine in TPP (using the Tandem analysis > > pipeline) and the database search works fine on the resulting *.tandem > > file. We're able to convert these files into *.pepXML format and view > > them in the PepXML Viewer without any problem. > > > We're unable however to analyse the *.pepXML data using XInteract. > > We'd like to run PeptideProphet then ProteinProphet, but each time we > > do the following error is generated: > > > ******************************************************************************************************************** > > run_in c:/Inetpub/wwwroot/ISB/data; c:\Inetpub\tpp-bin\xinteract - > > Ninteract.pep.xml -p0.05 -l7 -O c:/Inetpub/wwwroot/ISB/data/ > > 6hrs_Control_Dupl1-s1.tandem.pep.xml > > -------------------------------------------------------------------------------- > > > *********** > > > c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build > > 200909091257 (MinGW)) > > > running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" "c:/ > > Inetpub/wwwroot/ISB/data/6hrs_Control_Dupl1-s1.tandem.pep.xml" -L"7"" > > file 1: c:/Inetpub/wwwroot/ISB/data/6hrs_Control_Dupl1- > > s1.tandem.pep.xml > > processed altogether 3278 results > > > results written to file c:/Inetpub/wwwroot/ISB/data/interact.pep.xml > > > direct your browser tohttp://localhost/ISB/data/interact.pep.shtml > > > command completed in 1 sec > > > running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" > > MINPROB=0.05" > > (X! Tandem (k-score)) > > init with X! Tandem (k-score) trypsin > > MS Instrument info: Manufacturer: ABI / SCIEX, Model: unknown, > > Ionization: ESI, Analyzer: TOFMS, Detector: unknown > > > -------------------------------------------------------------------------------- > > ...skipping 20 lines of output... > > -------------------------------------------------------------------------------- > > > => Total of 0 hits. > > command completed in 0 sec > > > running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" > > command completed in 0 sec > > > running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" "c:/ > > Inetpub/wwwroot/ISB/data/PfalciparumAnnotatedProteins61.fasta"" > > - Searching the tree... > > - Linking duplicate entries... - Printing results... > > > - Building Commentz-Walter keyword tree...command completed in 1 > > sec > > > running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/ > > wwwroot/ISB/data/interact.pep.xml" > > > command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/ > > wwwroot/ISB/data/interact.pep.xml" failed: Unknown error > > > command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/ > > wwwroot/ISB/data/interact.pep.xml" exited with non-zero exit code: > > -1073741819 > > QUIT - the job is incomplete > > > command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -O > > c:/Inetpub/wwwroot/ISB/data/6hrs_Control_Dupl1-s1.tandem.pep.xml" > > failed: Unknown error > > > ******************************************************************************************************************************* > > > Is anyone able to assist in establishing what the problem is, and the > > best solution to follow? If need be we can ftp the error files > > generated by the command, or an example *.pepXML data file (<4Mb). > > > Thanks in advance > > > Tabo- Hide quoted text - > > - Show quoted text - --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
