Table 1.

Allowed post-translational modifications in the experimental proteogenomic design of TMT and iTRAQ experiments

Protocol	Modification(s)	Modification type
TMT	Cystine carbamidomethylation (+57.0215) and Lysine TMT labeling (+229.1629)	Fixed
TMT	Methionine oxidation (+15.9949), N-terminal protein acetylation (+42.0106), and TMT labeling of peptide N terminus and serine residues	Variable
iTRAQ	Cysteine carbamidomethylation (+57.0215), iTRAQ labeling of lysine (+144.10253) and peptide N terminus	Fixed
iTRAQ	Methionine oxidation (+15.9949)	Variable