Global Proteomics Analysis of Protein Lysine Methylation

Abstract

Lysine methylation is a common protein post-translational modification dynamically mediated by protein lysine methyltransferases (PKMTs) and protein lysine demethylases (PKDMs). Beyond histone proteins, lysine methylation on non-histone proteins plays a substantial role in a variety of functions in cells and is closely associated with diseases such as cancer. A large body of evidence indicates that the dysregulation of some PKMTs leads to tumorigenesis via their non-histone substrates. However, most studies on other PKMTs have made slow progress owing to the lack of approaches for extensive screening of lysine methylation sites. However, recently, there has been a series of publications to perform large-scale analysis of protein lysine methylation. In this unit, we introduce a protocol for the global analysis of protein lysine methylation in cells by means of immunoaffinity enrichment and mass spectrometry. © 2016 by John Wiley & Sons, Inc.

Keywords: immunoaffinity enrichment; mass spectrometry; methylation; non-histone; post-translational modification; proteomics.

Figure 1

The stepwise procedure for global proteomics analysis of protein lysine methylation.

Figure 2. Chromatogram of the SCX fractionation of peptides

A 60-min gradient (Table 1) was run to separation peptides.

Figure 3. An example of identification of methylated unique peptides and sites from a single experiment

The numbers of monomethylated (A), dimethylated (B) and trimethylated (C) unique peptides across 10 SCX are presented, respectively. (D) The identification number of three degrees of methylation sites.