Fig. 1: Methyl specific metabolic labeling for the proteomics discovery of methylation on diverse residues.

a Amino acid residues that can be methylated. b Workflow: Cells are differentially grown in light and methyl specific heavy Met, and are mixed at the ratio of 1:1 and lysed together. Proteins are digested with trypsin and analyzed by mass spectrometry. The methylated peptides are differentiated from methionine containing peptides by their different mass difference. By utilizing the correlation between the isotopic mass difference and the number of introduced methyl groups, the virtual MS/MS spectra corresponding to the unmethylated peptides are deduced by removing the mass of methylation modification in precursor mass and the MS2 peaks respectively. Then the extracted spectra are used for the methylation identification. c Example spectra for the in-silico demethylation approach. The twin peaks with identical mass were the peaks without methylation and the mass were kept, the twin peaks with a mass difference of 3*N were the peaks with methyl and the mass were kept after removing the mass of methyl. The deduced peaks were compared with the b or y ions for the identified sequence, showing that the ions without methyl can be deduced from the twin peaks with a mass difference of 3*N. d Methylated events identified in HEK293 cells and HepG2 cells. e The His methylation occurs exclusively on C3H1 ZF domains. Our Data: The information of total ZF proteins were obtained by subjecting our MS data to the traditional database searching. Deposited data: MS files of individually over-expressed ZF proteins were downloaded from the public database and analyzed. f Summary of identified methylated His peptides from C3H1 ZFs.