“…Mass spectrometry has been successfully used to identify even labile protein modifications, including protein phosphorylation 1–2 , and O-GlcNAc modifications 3–4 , as well as identifying chemical modifications including covalent labeling for protein surface mapping 5–6 , crosslinking 7–8 , deamidation of asparagine 9–10 , and protein oxidation 11–12 . In all of these systems, the amount of modification that occurs at each amino acid of a peptide or protein can have serious consequences to the interpretation of the data, whether for understanding chemical or enzymatic modification mechanisms and consequences 13–16 or for interpreting data from covalent labeling or chemical cross-linking studies 7, 17–20 .…”