Carlos, Unless I don't understand how XPRESS currently runs, I don't believe it will work on your separate light and heavy searches. This doesn't explain the failure to run error but it's worth mentioning up front. XPRESS expects a variable modification to denote the difference between your "light" peptides and your "heavy" peptides. I would suggest you run the search as follows: add static modifications n-terminus and lysine for light dimethyl and add variable modifications of 6.03 to both n-terminus and lysine. This way, you do a single search and identify both heavy and light at once in a format compatible with XPRESS. I believe you should be able to use ASAPRatio with your separate searches but I've not paid enough attention to that tool to be able to answer your question on how to set its options. If no one chimes in soon, search the archives of this group.
The failure to run XPRESS likely is associated with the error "Unknown file type. No file loaded." which I'm guessing means the corresponding spectral data (in say mzXML or mzML format) is not recorded in the .tandem.pep.xml files as the TPP expects. So it doesn't know what it is and can't read the spectral data. When naming conventions are not followed strictly, things tend to fall apart. Your <basename>.tandem.pep.xml file names worry me a bit as the standard convention is <basename>.pep.xml. Go ahead and send me one of your .tandem.pep.xml files directly (or make it available for me to download somehow) and I'll take a look as I suspect there could be an issue with the "base_name" attributes. And tell me what your Tandem xml files are named. Unless other Tandem/TPP experts chime in otherwise, try sticking to the following naming convention: Tandem file named: 1F0.xtan.xml pep.xml file named: 1F0.pep.xml (with "base_name" attribute value "1F0" or some variant of that i.e. "./1F0") mzXML file named: 1F0.mzXML - Jimmy On Wed, Dec 12, 2012 at 5:04 PM, Carlos <cchaves...@gmail.com> wrote: > Dear all > > I am trying to analyze my dimethylation data using XPRESS tool in TPP but > with no success so far... > > I did two XTandem searches for my mzXML files: one for light dimethyl > (+28@N-terminus and @K) and another one for heavy (+34@N-terminus and @K) > and merged them using the 'Analyze peptides' tab. > The PeptideProphet analysis worked fine, however when I check the 'Run > XPRESS' option I keep getting an error message (see bellow). > > running: "C:/Inetpub/tpp-bin/XPressPeptideParser > "XTANDEM_BR1_interact.pep.xml" -m0.5 -nn,6.032 -nK,6.032 -c6 -p1" > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > WARNING: Found more than one variable mod on N-terminus. > Unknown file type. No file loaded. > > command "C:/Inetpub/tpp-bin/XPressPeptideParser > "XTANDEM_BR1_interact.pep.xml" -m0.5 -nn,6.032 -nK,6.032 -c6 -p1" failed: > Unknown error > > command "C:/Inetpub/tpp-bin/XPressPeptideParser > "XTANDEM_BR1_interact.pep.xml" -m0.5 -nn,6.032 -nK,6.032 -c6 -p1" exited > with non-zero exit code: 255 > QUIT - the job is incomplete > > command "c:\Inetpub\tpp-bin\xinteract -NXTANDEM_BR1_interact.pep.xml > -p0.05 -l7 -OAN -d_R -X-m0.5-nn,6.032-nK,6.032-c6-p1 1F0.tandem.pep.xml > 1F0H.tandem.pep.xml 1F1.tandem.pep.xml 1F1H.tandem.pep.xml > 1F2.tandem.pep.xml 1F2H.tandem.pep.xml 1F3.tandem.pep.xml > 1F3H.tandem.pep.xml 1F4.tandem.pep.xml 1F4H.tandem.pep.xml > 1F5.tandem.pep.xml 1F5H.tandem.pep.xml F0.tandem.pep.xml F0H.tandem.pep.xml > F1.tandem.pep.xml F1H.tandem.pep.xml F2.tandem.pep.xml F2H.tandem.pep.xml > F3.tandem.pep.xml F3H.tandem.pep.xml F4.tandem.pep.xml F4H.tandem.pep.xml" > failed: Unknown error > Command FAILED > RETURN CODE:65280 > -------------------------------------------------------------------- > > My other question is regarding ASAPRatio > How to use it when performing dimethylation quantitation? I mean, since I > have two modifications for K (light and heavy dimethyl) and two for the > N-terminus, which residues should I set in the 'Change labeled residues > to' option and, also, which mass values should I set in the 'specified > residue mass' option? > > I am using the TPP v4.6 OCCUPY rev 1, Build 201209261035, installed on a > Windows 7 platform. > > I greatly appreciate any help. > > Best, > > Carlos. > > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/spctools-discuss/-/IdgmQ2DrvVMJ. > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > 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. 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