Hi, I want to analyze my shotgun proteome date using APEX, which requires a ProteinProphet XML file as an input.
First, I installed TPP 4.7.1 using the executable installer for MS Windows. (I'm currently using Windows 8.1 Professional x64, Korean; the ActivPerl version is 5.16.3.1604 [64 bit]) The Comet employed in this TPP version did not work with my mzML files, and I manually converted them using a Comet binary from http://sourceforge.net/projects/comet-ms/files/ Using the resulting XML files, I launched PeptideProphet in TPP and successfully obtained "interact.pep.xml" However, whenever I launched ProteinProphet with either the PeptideProphet file or the iProphet file, the program was abnormally terminated with the following message. *EXECUTING: c:\Inetpub\tpp-bin\ProteinProphet c:/Inetpub/wwwroot/ISB/data/interact.ipro.pep.xml c:/Inetpub/wwwroot/ISB/data/interact.prot.xml IPROPHET * ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.6 OCCUPY rev 3, Build 201307241109 (MinGW)) (xml input) (no FPKM) (report Protein Length) (using degen pep info) . . . reading in c:/Inetpub/wwwroot/ISB/data/interact.ipro.pep.xml. . . . . . read in 0 1+, 16500 2+, 4343 3+, 908 4+, 133 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. *Command FAILED* RETURN CODE:768 When I tried the conversion with an older version 4.6.3, the same result was obtained. (the message shown in above is obtained with TPP 4.6.3) I think this is not due to ActivePerl but ProteinProphet itself. I tried manual execution of ProteinProphet but it showed the same error message. Can anybody suggest a solution for this? I only have to generate the "interact.prot.xml" file. Thanks! Joungmin -- 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/d/optout.
