PeptideProphet

[Rishika Bisaria]

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

[David Shteynberg]

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

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[Rishika Bisaria]

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

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[Rishika Bisaria]

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