Matthias wrote: > Hi guys, > > Back here after a long break :-) I want to use the TPP for > quantitation of metabolic labeling experiments - both 14N/15N and 12C/ > 13C. I have two questions: > > 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. 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. > 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. --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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 -~----------~----~----~----~------~----~------~--~---
