Chemical Depletion of Histidine-Containing Peptides Allows Identification of More Low-Abundance Methylation Sites from Proteome Samples

Protein methylation, especially that
occurs on arginine and lysine
residues, is one of the most important post-translational modifications
involved in various cellular processes including RNA splicing, DNA
repair, and so forth. Systematic analysis of protein methylation would
facilitate the understanding of its regulatory mechanisms. Strong
cation chromatography has been used to globally analyze arginine/lysine
methylation at the proteome scale with good performance. However,
the co-enriched histidine-containing peptides severely interfere with
the detection of low-abundance methylpeptides. Here, we developed
a novel chemical strategy which enabled almost complete depletion
of histidine-containing peptides in the protein digest, thereby resulting
in the identification of more low-abundance arginine/lysine methylpeptides.
Totally, 333 arginine and lysine methylation forms from 207 proteins
were identified in this study. Overall, the number of methylation
identifications increased about 50% by using our new method. Data
are available via ProteomeXchange with the identifier PXD023845.