Deep profiling of lysine methylation by covalent enrichment-enhanced proteomics

Lysine methylation is a classic posttranslational modification, yet most studies focus on histone methylation. Although emerging evidence demonstrates the significance of nonhistone lysine methylation, current approaches that investigate individual proteins of interest are relatively low throughput. Proteomics provides an ideal strategy for comprehensively studying cellular posttranslational modifications, but current enrichment methods typically allow the identification of only a few hundred methyllysine sites because of insufficient enrichment efficiency for low-abundance methyllysine-containing tryptic peptides. Here we report a comprehensive lysine methylation profiling method based on covalent enrichment-enhanced quantitative proteomics, termed DEKmeP. In practice, DEKmeP enables systematic nomination of candidate substrates and their monomethylation sites regulated by lysine methyltransferases. Through subsequent biochemical and cellular experiments, we validate dozens of nonhistone substrates of lysine methyltransferases. Moreover, we characterize the functional effects of SMYD2-mediated c-Jun K288 methylation. Therefore, DEKmeP may shift lysine methylation studies from the investigation of individual proteins of interest to systematic exploration of the methyllysine proteome, thereby expanding the understanding of lysine methyltransferase catalysis and nonhistone lysine methylation. The authors report DEKmeP, a covalent enrichment-based quantitative proteomics workflow for deep lysine methylation profiling enabling systematic nomination of methyltransferase-regulated sites.