I'm a new member on Scientist Solutions and would like a solution to my problem. I have a highly abundant Coomassie stained protein which is in the form of a SDS-gel band. I have performed in-gel digestion with this band several times and do not get any ions in MS/MS. The intensity of the MS spectrum is low. However, a control band from the same gel with comparable MS intensity is getting fragmented and identified. What could be the problem? Can I do something to ensure that some of the peptides do fragment?