Jagan, Start with your mzXML file. Generate mgf using "MzXML2Search -mgf yourfile.mzXML". Use this to do your omssa search and hopefully this fixes your problem.
Compare the TITLE lines of the mgf generated by MzXML2Search with your "standard" mgf you used for the search. That difference is the reason why you can't see spectra as the required encoded information (mzXML base name and scan #) are likely not in the mgf file you used to search. Without this information encoded in a specific way, there's no way that the TPP will know which spectrum belongs to which peptide ID. Good luck! (Also, you should be able to export pep.xml directly from omssa using the "-op" option but presumably this isn't a part of the problem.) On Thu, Nov 4, 2010 at 7:14 PM, Jagan Kommineni <[email protected]>wrote: > Dear All, > > I havn't received my presvious message myself as the memeber of this group > and hence i am here with sending once again. > > Soory for the inconvinience if you already received my previous message. > > > Here is my previous message: > ======================= > > On Thu, Nov 4, 2010 at 5:06 PM, Jagan Kommineni <[email protected] > > wrote: > >> Dear All, >> >> I would like to view the OMSSA results with pepXMLViewer as there some >> compatibility issues with the latest version of OMSSA and OMSSA Browser. >> >> I have taken standard mgf file and run OMSSA search against it and >> produced xml formatted output. >> >> Then I have used omssa2pepXML (part of the OMSSA distribution) to generate >> pepXML file. I have also generated mzXML file using latest version of the >> msconvert from the build of ProteoWizard release: 2.1.2351 (2010-11-3) on >> Linux box. >> >> I am able to view pepXML file using pepXML Viewer, but few things are >> missing. When I click first few rows of the "IONS" column I am able to view >> the display (not sure how much extent this display is correct) but after >> that when I click any item in the same column I am getting an error message >> "Error-cannot parse scan number ...". >> >> I suspect this is due to the fact that the mzXML was generated from mgf >> file which itself doesn't contain retention time information. >> >> I wonder is there anyway I can able to produce reasonable views with mzXML >> file generated from the mgf file. >> >> Please note that I didn't have these problems when I produce mzXML file >> from the RAW files. >> >> >> >> >> >> >> >> >> >> with regards, >> >> -- >> Dr. Jagan Kommineni >> Systems Administrator and Duty Programmer >> Australian Proteomics Computational Facility >> Ludwig Institute for Cancer Research, >> 6th Floor, Royal Melbourne Hospital, >> Royal Parade, Parkville, Victoria >> Ph:03 9341-3177. >> >> > > > -- > Dr. Jagan Kommineni > Systems Administrator and Duty Programmer > Australian Proteomics Computational Facility > Ludwig Institute for Cancer Research, > 6th Floor, Royal Melbourne Hospital, > Royal Parade, Parkville, Victoria > Ph:03 9341-3177. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]<spctools-discuss%[email protected]> > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
