Hi , I successfully ran the PeptideProphet and have got the output pepxml file.But I am getting stuck in ProteinProphet step.
ProteinProphet C:\Inetpub\wwwroot\ISB\data\output1.2013_07_20_15_59_46.pep.xml C:\Inetpub\wwwroot\output_xtandem\output1.2013_07_20_15_59_46.xml ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.6 OCCUPY rev 2, Build 201302140902 (MinGW)) (xml input) (report Protein Length) (using degen pep info) . . . reading in C:/Inetpub/wwwroot/ISB/data/output1.2013_07_20_15_59_46.pep.xml. . . . . . read in 0 1+, 0 2+, 207 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. Regards, Rishika On Mon, Jul 22, 2013 at 4:20 PM, Rishika Bisaria <[email protected]>wrote: > Hi , > Thank you for the reply.I tried converting the output of XTandem using TPP > pipeline but it is not accepting the file.Is there any other conversion > method by which I can convert the same into pepxml. > > Regards, > Rishika > > > On Mon, Jul 22, 2013 at 3:06 PM, David Shteynberg < > [email protected]> wrote: > >> Tandem's native xml format is different from pepXML format needed by the >> TPP. Please convert your tandem.xml files to pepXML first, this should >> happen automatically if you run the search through the TPP. Otherwise you >> can use the Analysis Pipeline->pepXML tab to convert. >> >> -David >> >> >> On Mon, Jul 22, 2013 at 11:24 AM, Rishika Bisaria < >> [email protected]> wrote: >> >>> Hi, >>> I have successfully obtained output xml file from XTandem and when Ia m >>> trying to use that file as an input for PeptideProphet I am getting an >>> error did not find closing tag "</msms_pipeline_analysis>". >>> >>> >>> C:\Users\ribisari\Desktop\Downloads>PeptideProphetParser >>> C:\Users\ribisari\Desktop\Software\tandem-win-13-06-15-1\tandem-win-13-06-15-1\bin\output.2013_07_20_15_59_46.t.xml >>> MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: >>> UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN >>> >>> Error: file update failed (did not find closing tag >>> "</msms_pipeline_analysis>"), check file >>> C:\Users\ribisari\Desktop\Software\tandem-win-13-06-15-1\tandem-win-13-06-15-1\bin\output.2013_07_20_15_59_46.t.xml.tmp.a >>> 12628 for completeness >>> error: no peptideprophet data written to file >>> C:\Users\ribisari\Desktop\Software\tandem-win-13-06-15-1\tandem-win-13-06-15-1\bin\output.2013_07_20_15_59_46.t.xml >>> >>> Kindly let me know what should I do to proceed ahead. >>> >>> Regards, >>> Rishika >>> >>> -- >>> 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 a topic in the >> Google Groups "spctools-discuss" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/spctools-discuss/4MIq-sKq9_E/unsubscribe >> . >> To unsubscribe from this group and all its topics, 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.
