Hi Carlos, Do your searches using Tandem as Jimmy mentioned setting the light mod as a *static* on [ and K, then the difference between the light and heavy as the *variable* mod on [ and K. This is in the Tandem API here: http://www.thegpm.org/tandem/api/rmm.html. The Tandem API describes a static mod as "residue, modification mass" and variable as "residue, potential modification mass."
When using ASAPRatio, do not tick the Static option. Select "n" and "K" in the "Change labeled residues to" line. Then below change the "Specified Residue Mass 1" to be the monoisotopic mass of the heavy modification on the n-Terminus (e.g. 34 in your case) and for the ".... Residue Mass 2" to be the monoisotopic mass of the modified lysine e.g. residue mass of K + the heavy mod. ASAPRatio will throw out a warning about having multiple mods on K... but its a warning not an error and seems to be reminding the user to be certain to specify a heavy mod, which if you followed the above instructions you will have already done. You should be good to go then. Most of the computation time is spent on the last step running the asapproteinratio parser. On a ~0.25 million spectra search, it takes about a half hour or so to complete on a core i7 laptop. Cheers, Brian On Wed, Dec 12, 2012 at 8:04 PM, Carlos <[email protected]> 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 [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. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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