I was initially skeptical when a friend told me I should check out this paper.
I've been down the microwave digestion route before. And, while I may have primarily been young(er) and stupid(er), I still believe that the microwave cooked off my phosphorylations.
However -- this new study is pretty convincing that the technique has real value!
Unlike enzymatic digestion which will occur reliably at specific residues, put some formic acid in with your proteins and microwave them -- and the proteins break all over the place. Reactive oxygen/ I don't know, but it does really work. (but it might cook off the phosphos first )
In this study these authors use the method for analysis of single proteins (including mABs) and get such a nice overlap in coverage that they can sequence the proteins de novo!