iTRAQ is quantified based on ms/ms fragment peaks; use the Libra tool for that labeling method. ASAPRatio and XPRESS are not meant to work on iTRAQ data.
As for O18 labeling, under the presumption that two O18 atoms are incorporated into the heavy labeled peptides, you want to specify a 4 Da mass shift occurring at the C-terminus of each peptide. In the TPP GUI for XPRESS, check the checkbox to RUN XPRESS and choose 'c' (for c-terminus) and 4.0 mass difference. For ASAPRatio, change the labeled residue to 'c'. I *think* this is all you need for ASAPRatio. Your database search should either contain identifications for both light and heavy peptides using a variable 4 Da modification on the c-terminus. Or the search can just be of light (normal/O16) peptides if you can't do a variable c-term modification search. - Jimmy Bright wrote: > Hi everyone > I do not know how to use the parameter about residue mass > different in XPress and ASAPRatio. Expecially, the sample has been > labeled by O18. For example, if peptide has been labled by O18 or > iTRAQ, how to set the different residue mass parameter in TPP > according to different label model. The parameter one is "Change > XPRESS residue mass difference" in XPRESS the other is "Specified > residue mass" in ASAPRatio. If possible, could you show a example for > me. > > Thank very much. > > Bright --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
