UNIT 14.9 Identifying and Quantifying Sites of Protein Methylation by Heavy Methyl SILAC

  1. Shao-En Ong1,
  2. Matthias Mann2

Published Online: 1 DEC 2006

DOI: 10.1002/0471140864.ps1409s46

Current Protocols in Protein Science

Current Protocols in Protein Science

How to Cite

Ong, S.-E. and Mann, M. 2006. Identifying and Quantifying Sites of Protein Methylation by Heavy Methyl SILAC. Current Protocols in Protein Science. 46:14.9:14.9.1–14.9.12.

Author Information

  1. 1

    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts

  2. 2

    Max Planck Institute for Biochemistry, Martinsried, Germany

Publication History

  1. Published Online: 1 DEC 2006
  2. Published Print: NOV 2006


A new appreciation of protein methylation comes with the recent discovery of demethylases, now placing methylation in the realm of a transient, reversible modification. Classical approaches to study methylation are laborious and involve radioactive, in vitro, enzyme-substrate labeling experiments with purified proteins. Mass spectrometry–based proteomics allows the unbiased analysis of complex protein mixtures and is increasingly applied to the study of post-translational modifications. However, it is particularly challenging to study methylation by proteomics because of the number of residues affected and the degree of methylation that can occur. Heavy methyl SILAC is a metabolic labeling strategy that harnesses the cell's machinery to convert a nonradioactive, stable isotope labeled version of methionine into the ‘heavy’ biological methyl donor S-adenosylmethionine. Cells incorporate this ‘heavy’ methyl group throughout their methylated substrates. This technique increases confidence in identifying and quantifying of sites of protein methylation.


  • SILAC;
  • mass spectrometry;
  • proteomics;
  • metabolic labeling;
  • methylation;
  • quantification;
  • post-translational modification