Hi,

probably one of the earliest works and still an excellent reference is this publication from Yates and colleagues:

http://www.pnas.org/content/99/12/7900.long

If you are interested in phosphorylation, a recent paper that I co-authored could be useful for you:

http://jcb.rupress.org/content/206/4/541.long

It refers to several papers from the group of Eberhard Krause that contain more thorough descriptions of the employed workflow

1) I would split my sample in two aliquots

2) I would dephosphorylate or deglycosylate one and keep the other one as control

3) I would perform proteolysis compare hydrolysates between treated and untreated aliquots. (repeat for each protease you're willing to use)

for dephosphorylation this protocol was very effective (I used calf intestine alkaline phosphatase from SIGMA, cat P6674):

http://www.abcam.com/protocols/protein-dephosphorylation-protocol

and for deglycosylation I used the SIGMA Enzymatic protein deglycosylation kit (Cat. EDEGLY) following the product instructions.

Thanks a lot for the answers. As this is about protein methylation and not phosphorylation some of it won`t work unfortunately. I really like the idea of comparison with part of the sample where the PTM has been removed, but I don`t think it`ll work. The papers are a good starting point - thanks again.