Dear TPP team: I'm wondering if anyone can help to troubleshoot the issue with OMSSA and iprophet. here is my workflow: Raw data converted to mzXML by ProteoWizard msConverter. Using these mzXMLs, I have no problem to combine Tandem and Comet results by iprophet though. mgf generated by TPP from mzXML fasta database containing decoy sequences were converted by makeblastdb.exe. Search by OMSSA and convert omx output to pep.xml by OMSSA2pepXML.exe
edit XML elements at the start of the pep.xml to reflect the source database and input mzXML before .fasta and .mgf conversion respectively. For peptideprophet, -Selete accurate mass binning(ppm) -Selete "Use decoy hits to pin down the negative distribution.Decoy Protein names begin with: DECOY" -Selete "Use Non-parametric model (can only be used with decoy option)" add -ELysc -C -P -M To this point everything works OK, but I can not get this OMSSA results through iprophet, whether by itself or with other results from Comet or tandem. usually I get error message like this, which does not explain too much command "c:\Inetpub\tpp-bin\InterProphetParser c:/Inetpub/wwwroot/ISB/data/ecoli/lysc_omssa_sax_01.pep.xml c:/Inetpub/wwwroot/ISB/data/ecoli/lysc_tandem_sax_01.pep.xml lysc_omssa_tandem_sax_01.ipro.pep.xml" failed: Unknown error Command FAILED RETURN CODE:65280 I'm wondering if I did anything wrong that cause this problem. THank you! SunSun -- 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.
