Hi Jimmy, thanks for the quick reply.
> > 1.) Is it possible to use 13C labeling with either XPress or > > ASAPRatio? I've found only options for 15N, so is there any chance to > > process 13C-labeled samples? > > You can't analyze 13C labeling now with Xpress. I don't see 13C (nor > 15N) support mentioned in the ASAPRatioPeptideParser usage statement so > there's a decent chance you can't use ASAPRatio right now for 13C > analysis either. Okay, now I've also seen that 15N support is not mentioned in the ASAPRatio usage statement. I was quite sure that I have read about 15N support for ASAPRatio in the announcement of TPP4.2. Perhaps I was just fantasizing. > > It was easy to extend the 15N option in Xpress to 13C labeling which I > just did with the source files I have checked out. But it might take > awhile before these changes make it out. I need to check in the mods, > we'll need a small TPP GUI update, and the next TPP release will need to > be released. Oh, this would be great if your modifications were available. For the moment I would also be happy if you could just check in the files so I could get them and compile them here (or, if you don't mind, even mail them to me. I have some people here urgently waiting for some results...). I would also do some beta- (or alpha-) testing of the new feature ;-) > > > 2.) How to perform the searches (Mascot in my case)? As far as I > > understood I have to search each sample twice - once for the light and > > once for the heavy peptides. That means to modify the masses and > > modification files on the Mascot server for every heavy search, so it > > is quite uncomfortable, especially if the Mascot server is shared with > > a lot of other people... With version 2.2, Mascot offers an option for > > metabolic labeling, resulting in the identification of light and heavy > > peptides in one run. Is it possible to process such a combined result > > file through the TPP? > > For current Xpress analysis of metabolic labeled samples, the searches > do need to be performed separately. > > I don't know how the modification specification in pepXML handles > metabolic labeling and if the Mascot to pepXML converter can correctly > translate combined light/heavy metabolic search results to pep.xml > files. It's going to take time and effort from some volunteer to make > it possible to process a combined result through the TPP. Okay, that's what I expected. After doing some seperated searches now I have the impression that the pepXML does not handle metabolic labeling at all. For heavy peptides, the Spectrum view (plot-msms) shows complete nonsense. Also the mass of modifications on heavy peptides is wrong - methionine oxidation is recorded with a mass of 147 but should be 148 on an N15 peptide. Or have I done something wrong with the Mascot search or conversion? Regarding Samy's mail, I have also found that the XPressDisplay shows only the light peptides. I think there is a bug in XPressCGIProteinDisplay.cxx - double use of the int k in two nested for loops. I can provide a fixed version if someone is interested ;-) Best wishes - Matthias --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
