> Similarly, if > only the difference between light and heavy residues are entered for > XPRESS, how does this program know the mass of the light and heavy > tagged residues?
Regarding this question, XPRESS doesn't need to know the mass of the tagged residues as that information isn't necessary. Knowing the labeled residues which you specify, it determines if a peptide is the light or heavy form based on the modifications from the search because you have to run the search in a specific way. Peptides with no variable modifications on the specified residues are "light" and peptides with variable modifications on all of the specified residues are "heavy". The mass of the identified peptide is known and calculated from the database search. XPRESS just needs to get the mass of the paired peptide now. Once it knows that a peptide is either light or heavy, it can calculate the m/z of the corresponding pair by counting the number of labeled residues in the peptide (which it knows 'cause you specified the labeled residues) and their mass difference (which you also specify). The # of labeled residues and mass difference gives the mass to either add or subtract from the identified peptide mass to calculate the mass of the other pair. Hope I explained this clearly and hopefully someone else will chime in on your ASAPRatio questions. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-disc...@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.
