on the list of things that I'm glad no one has asked me to do today and I would probably have laughed and said "...ask me again in 10 years..." I present --
I mostly know about Fast Photochemical Oxidation of Proteins because the Queen of FPOP, Dr. Lisa Jones is right downtown doing crazy amazing protein structural stuff IN LIVING ORGANISMS with the technique. Or was, because Jones lab is leaving the world's greatest city and is heading to crummy UC San Diego. (Congratulations, UCSD!)
FPOP can induce a lot of different alterations on the exposed protein regions while largely not affecting any parts of the protein that are folded in such a way that they are on the inside of the protein and can't be attacked by these oxidation events.
This is a tough technique for bottom up and special software exists just for this technique. But top down? Which is already hard enough??
How do you get that data? They chopped up the DNA so it was off of their modified protein and they used a 15(!!) TESLA magnet for top down with CID and EAD. They also did bottom up traditional FPOP style so they had a good lead on the mods.