I also need to plot all single-peptide protein IDs for MCP publication (~ 400 annotated spectra). My ProteinProphet output is a combination of four large mzXML files. When I try to manually get to the spectra views, the program produces a blank page from the call ending with "FileName=C:/firstfile/+C:/nextfile+C:/thirdfile/+C:/lastfile" If I delete the files from that string that do not contain the peptide, then I can plot the spectra.
Has the batch plotting mentioned in this thread been included in more recent TPP versions? Best wishes, Jesse On Wednesday, August 25, 2010 11:14:22 AM UTC-7, Damaris Bausch wrote: > > Thanks for all the answers! > > I actually found someone nearby, that was able to generate the > spectral images. > > Of course it would be great if MCP would accept Skyline as spectral > viewer in the future. This would make things much easier. Or anyway, > if they would loosen their criteria in this regard, too.... > > -Damaris > > > On Aug 24, 8:40 am, Brendan <[email protected]> wrote: > > Hi Damaris, > > I should note that one of the features to which Birgit refers, the m/z > > value annotations was recently added to my development release for > > Birgit to test, and will not be freely available in the public release > > until I make the next public release, which I expect to be a little > > over 2 weeks from now. Before then, Birgit and I will be at a meeting > > where we will try to discuss this approach with an MCP editor who has > > expressed interest in this idea in the past. > > > > Skyline does support building these libraries from pepXML and mzXML > > from the TPP, as well as directly from Mascot .dat file, X! Tandem > > XML, Protein Pilot .group files, etc. We'll probably add a step-by- > > step instruction page, once we are sure this will be acceptable to > > MCP, but this will still likely be a couple weeks. > > > > If you are interested, you could play around with building your > > library now. > > > > --Brendan > > > > On Aug 23, 4:43 pm, Birgit <[email protected]> wrote: > > > > > > > > > Hi Damaris, > > > > > I actually often have similar considerations. I recently worked with > > > Brendan MacLean from the Open Source Program Skyline (MacCoss lab) > > > which is a freely available software. It is available under > > > > > Skyline :http://proteome.gs.washington.edu/software/skyline, B. > > > MacLean, M.J. MacCoss et al > > > > > One can import spectral libraries from any discovery datasets in a > > > very straightforward way, and then display the MSMS from any of the > > > identified peptides in an interactive way, with fragment ions > > > annotated with ion types and observed m/z values. As far as I know > > > recently MCP also allows for "Spectral Viewers", which Skyline should > > > qualify for. > > > > > Let me know if you are interested or Brendan MacLean can also be of > > > help in this ...., one can contact Brendan through > > > his support page that is part of the Skyline homepage: > https://brendanx-uw1.gs.washington.edu/labkey/project/home/support/be... > > > > > Regards, > > > Birgit > > > > > On Aug 22, 1:43 pm, Damaris Bausch <[email protected]> wrote: > > > > > > Hi, > > > > For a MCP publication I need to export all MS/MS spectras into > images. > > > > Is there somewhere a script available that does that autimatically? > > > > The data has been processed with the TPP. > > > > > > Thanks, > > > > Damaris -- 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/groups/opt_out.
