To edit lysine, click on the composition of Lys and select the small calculator button to open the elemental composition editor. Setting the SILAC 13C6 lysine residue, you set Carbon to 0 (zero) and the newly created Carbon13 C3/Cx to 6. Select OK and edit any other residues that need to be changed (e.g. arginine for the typical SILAC experiment).
You then select the Save as button and save the the table as a new residue mass file (e.g. with the name SILAC). Close the dialog, close GPMAW and restart the program, and the new mass file will be available for selection in the drop-down box in the main toolbar.
Working with both heavy and normal residues:
If you need to work with normal and heavy residues in the same sequence, you need to define the heavy residues as new residues, using the positions 21 to 30 in the residue mass table. Remember that each residue needs a unique 1-letter code to function. Save the file under a new name.
You then have to edit your sequence to put the heavy residues into place.
If you ‘just’ want to compare the mass values of normal and heavy residues, you can do that in the peptide list (from a digest) by using the secondary mass table feature of the peptide window.