Using affinity purification coupled with stable isotope labeling by amino acids in cell culture quantitative mass spectrometry to identify novel interactors/substrates of protein arginine methyltransferases

Methods. 2020 Mar 15;175:44-52. doi: 10.1016/j.ymeth.2019.11.015. Epub 2019 Nov 30.


The protein arginine methyltransferase family (PRMT) is known as being the catalytic driving force for arginine methylation. This specific type of post translational modification is extensively used in biological processes, and therefore is highly relevant in the pathology of a profusion of diseases. Since altered PRMT expression or deregulation has been shown to contribute to a vast range of those diseases including cancer, their study is of great interest. Although an increasing number of substrates are being discovered for each PRMT, large scale proteomic methods can be used to identify novel interactors/substrates, further elucidating the role that PRMTs perform in physiological or disease states. Here, we describe the use of affinity purification (AP) coupled with stable isotope labeling with amino acids in cell culture (SILAC) quantitative mass spectrometry (MS) to identify protein interactors and substrates of PRMTs. We also explore the possibility of exploiting the fact most PRMTs display lower dissociation rates with their hypomethylated substrates as a strategy to increase the proportion of substrates identified in AP/MS studies.

Keywords: Affinity purification/Mass spectrometry (AP/MS); Arginine methylation; PRMT; PRMT inhibitor; SILAC.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / metabolism
  • Arginine / analysis
  • Arginine / chemistry
  • Arginine / metabolism
  • Chromatography, Affinity / methods*
  • Enzyme Inhibitors / chemistry*
  • Gene Expression
  • Histones / chemistry
  • Histones / metabolism
  • Humans
  • Isotope Labeling
  • MCF-7 Cells
  • Mass Spectrometry / methods*
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism
  • Protein Binding / drug effects
  • Protein-Arginine N-Methyltransferases / antagonists & inhibitors*
  • Protein-Arginine N-Methyltransferases / chemistry*
  • Protein-Arginine N-Methyltransferases / genetics
  • Protein-Arginine N-Methyltransferases / metabolism
  • Proteomics / methods*
  • Recombinant Proteins


  • Amino Acids
  • Enzyme Inhibitors
  • Histones
  • Nuclear Proteins
  • Recombinant Proteins
  • Arginine
  • PRMT6 protein, human
  • Protein-Arginine N-Methyltransferases