Error with ProteinProphet

[Rishika Bisaria]

Hi,

I am able to run successfully the TPP pipeline on one of the mzXML file.But on using TPP on other mzXML file , ProteinProphet is throwing error stating that did you forgot to run PeptideProphet.

I have crossed checked all the parameters , they are correct.I am using the latest version of TPP on windows and running it using commandline.

1.tandem input.xml

2.Tandem2XML output.2013_07_24_13_24_28.t.xml output.2013_07_24_13_24_28.pep.xml

3.PeptideProphetParser output.2013_07_24_13_24_28.pep.xml MINPROB=0.2

4.ProteinProphet output.2013_07_24_13_24_28.pep.xml c:\Inetpub\wwwroot\out1.prot.xml

P.S. Everytime I am changing the parameters in input.xml file.I am using k-score function.

Thanks,

Rishika   

[David Shteynberg]

You pipeline is missing the InteractParser step.  Once you have a pep.xml file from Tandem you can run "xinteract -ip -p0 "on it to generate InteractParser->PeptideProphet->iProphet->ProteinProphet pipeline results.

-David

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[Rishika Bisaria]

Hi,

Thank you for the reply.

Actually I want to follow this pipeline:

Tandem->peptideprophet->q3new->proteinprophet->Q3proteinRatioParser.

And also when I am using Xinteract , I am getting the below error:

running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.iproph.pep.xml"

Analyzing interact.iproph.pep.xml ...

Reading NSS model  ...

Reading NRS model  ...

Reading NSE model  ...

Reading NSI model  ...

Reading NSM model  ...

Reading NSP model  ...

Parsing search results "SP062512_062912_IP0201_AX01_23to24 (X! Tandem (k-score))"...

  => Total of 0 hits.

  => Total of 0 decoy hits.

  => Total of 0 excluded hits.

command completed in 1 sec

running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/xtandem/interact.iproph.pep.xml"

command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/xtandem/interact.iproph.pep.xml" failed: Unknown error

command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/xtandem/interact.iproph.pep.xml" exited with non-zero exit code: -1073741819

QUIT - the job is incomplete

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[David Shteynberg]

Any reason you would see this other than Tandem search failed to generate results?

Parsing search results "SP062512_062912_IP0201_AX01_23to24 (X! Tandem (k-score))"...

  => Total of 0 hits.

  => Total of 0 decoy hits.

  => Total of 0 excluded hits.

[Rishika Bisaria]

I am sorry but I am really very new to Proteomics and I am not able to figure out the reason for error.

[David Shteynberg]

Usually when the search returns no good results (which is what TPP is telling you here) it is one of three possible options:

1.  Bad data quality 

2.  Wrong search parameters (incorrect static mass mod or wrong enzyme info. etc)

3.  Wrong database (incorrect organism etc)

Please consider these possibilities in your search results.

-David

[Rishika Bisaria]

Thank you.Will look into the parameters again.

Regards,

Rishika