Thanks for your help Jimmy and Ben. I solved this problem. I
searched the files using MASCOT with the monoisotopic mass of the
light tags set as Fixed modifications and the monoisotopic mass of the
heavy tags set as Variable modifications. In the dat file, MASCOT
lists the mass difference
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
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
In the MASCOT search, I specify a variable modification for the n-
terminus and lysine residue for both light and heavy tags. This
allows for the identification of unlabeled peptides. In this
framework, no variable mods is unlabeled, whereas variable mod with an
addition of 140 Da is light and
Hi Mike,
Not sure if this is helpful or not but I've been able to make ASAPratio work
with binary chemical labeling (reductive dimethylation in my case) by doing
two separate searches with the light label specified as a static mod in one
and the heavy label specified as a static mod in the other.
In the scenario you describe, XPRESS would think that all of the
identified peptides were heavy and quantify the corresponding light
partner by always subtracting a mass from the identified peptide mass.
So check your results to confirm whether or not this is the case; I'd
have to think that half
