Determining light or heavy peptide is simple and shouldn't be a black box: No variable mods on the specified residues equals light peptide. Variable mods on all of the specified residues equals heavy peptide. If there's a mixture (in your case an unmodified + a modified lysine in the same peptide), then that peptide is ignored.
On Fri, Oct 22, 2010 at 2:20 PM, Mike <michael.gorm...@gmail.com> wrote: > Thanks for your prompt reply Jimmy. It is clear to me how XPRESS > calculates the mass difference between light and heavy labeled > peptides. As you describe, this is simply a matter of knowing the > number of labeled residues in the peptide and the associated mass > differences. It is unclear how the program identifies whether a > peptide is light labeled or heavy. For instance, let us say that I > have detected a doubly charged peptide at an m/z of 900. If this is > the light labeled peptide, I would expect to see the heavy labeled > peptide pair at an m/z of 904. If this is the heavy labeled peptide, > I expect to see the light labeled pair at an m/z of 896. I can assume > that XPRESS obtains the information regarding whether a peptide is > light or heavy labeled based on which variable modifications match the > spectra in the MASCOT search. This aspect of the analysis is working > however, so I am content to keep this process in a black box. > > I suspect my problems with ASAP ratio come from discrepancies in the > way the Mascot search was done and what ASAP ratio expects to find in > the pepXML file. > > On Oct 22, 4:53 pm, Jimmy Eng <jke...@gmail.com> wrote: >> > 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. > > -- 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.
