Hi all,
I am trying to use xpress to quantify peptides that have SILAC labeled
lysine and variable diglycine on lysine. When I run Xpress with the
following command:
C:\Inetpub\tpp-bin\XPressPeptideParser c:[path
removed]\UV0.all.ptmtest1.interact.ptm.pep.xml -m0.05 -nK,8.014199 -c5 -p1
Xpress incorrectly chooses whether the calculated peptide mass is
heavy/light when diglycyl-lysine or heavy lysine are present in the
peptide. (1) If the peptide only has heavy lysines and no
diglycyl-lysine, then xpress sets the calculated mass to the light. (2)
If the peptide has only light lysine and a diglycyl-lysine modification,
xpress sets the calculated mass as heavy. (3) If the peptide has both
heavy lysine and at least one diglycyl-lysine, xpress assigns the
calculated mass as the light value. (4) If the peptide contains no
diglycine and no heavy lysine.
Any help would be appreciated.
Best regards,
Jesse
--
Jesse Meyer
Graduate Student
Department of Chemistry and Biochemistry
University of California, San Diego
La Jolla, CA 92092
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