A new chromatographic approach to analyze methylproteome with enhanced lysine methylation identification performance

Highlights: • Cu-IMAC depletion of His-containing peptides improved methylproteome coverage. • Low pH SCX fractionation enhanced lysine methylation identification performance. • Large-scale dataset revealed new motif of lysine methylation. -- Abstract: Arginine/lysine methylation is an important post-translational modification (PTM) involved in DNA repairing, transcriptional regulation, etc. Immunoaffinity enrichment is currently the most widely used methods for the methylproteome analysis. Large-scale analysis of arginine methylation has been realized by using pan-R-methyl antibodies. Unfortunately, pan specific antibodies targeting all three lysine methylation forms are not available. In this study, we presented a novel chromatography-based enrichment method for global methylproteome analysis. The offline multidimensional tandem chromatography combining strong cation exchange (SCX) chromatography, immobilized metal ion affinity chromatography (IMAC) and high-pH reversed-phase chromatography (high-pH RP) was applied in the large-scale analysis of methylproteome. Totally, 860 forms on 765 sites were identified from BEL cells, covering all five arginine/lysine methylation forms. Among them, 27.21% were lysine methylation forms. This technique allows the simultaneous analysis of both arginine and lysine methylation while it has improved performance for the identification of lysine methylation. Therefore, it is a promising strategy for the investigation of biological functions related to methylation.