Hi,
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?

Thanks.

What are your MS conditions? And how are you introducing the sample into the MS?

There are many factors that can suppress MS response. The problem could be with the sample, the introduction technique, or the MS.

Please give us more information on the digestion step.