When running a MALDI-TOF mass analysis of a tryptic digest of a protein
band where the coomassie blue was not completely removed, what does one
see?
Coomassie blue peak at mass 832?
Peptide fragments that are incomplete cleavages dues to competition of the
CB for the basic residues?
Suppression of MALDI signal due to the presence of CB in the sample with
matrix?
The addition of CB mass (832) (or multiple 832 additions) to peptide
fragment masses?
Obviously, running LC/MS is the way to go, to pull out the separate CB
peak from the other peptides--but using a Zip-tip on this sample, it seems
that the interesting peaks are eluting in the step-wash that brings out
some blue--I'm curious as to what to expect in the MALDI spectrum. I am
seeing partial cleavages--and mostly doubly charged ions, not singly
charged ions using sinapinic acid for the matrix.
I am interested in both the CB effects and suggestions for running CNBr
cleaved samples--we are trying to track a degradtion that happens in a sea
of lysines and arginines--so I want to avoid the lys and arg cutters for
this problem. May go to endo glu c if CNBr digests are notoriously messy.
Thanks,
Deb McMillen
Institute of MOlecular Biology
University of Oregon
Eugene OR 97405