> 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.

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