If you want to direclty compare two LC/MS data sets, we use a different
approach that is a little cumbersome, but actually fairly easy to do. We
print out a contour plot of data with m/z vs elution time, where pixel
density represents signal intensity. We then scan it and use a program for
analyzing 2D gels (we use melanie II, but you can also use flicker for free
on the web). This only spots the differences, we have to go back to the
original data to identity the mass of the peptide that is changed. I also
prefer to do quantitation of differences with the MS software, rather than
with melanie.
In my opinion, the best quantitative index for peptide mapping is the
extent of coverage (residues in peptides/total residues in protein X 100).
Katheryn Resing