Quantitative chemical proteomics approach to identify post-translational modification-mediated protein-protein interactions

J Am Chem Soc. 2012 Feb 1;134(4):1982-5. doi: 10.1021/ja210528v. Epub 2012 Jan 24.


Post-translational modifications (PTMs) (e.g., acetylation, methylation, and phosphorylation) play crucial roles in regulating the diverse protein-protein interactions involved in essentially every cellular process. While significant progress has been made to detect PTMs, profiling protein-protein interactions mediated by these PTMs remains a challenge. Here, we report a method that combines a photo-cross-linking strategy with stable isotope labeling in cell culture (SILAC)-based quantitative mass spectrometry to identify PTM-dependent protein-protein interactions. To develop and apply this approach, we focused on trimethylated lysine-4 at the histone H3 N-terminus (H3K4Me(3)), a PTM linked to actively transcribed gene promoters. Our approach identified proteins previously known to recognize this modification and MORC3 as a new protein that binds H3M4Me(3). This study indicates that our cross-linking-assisted and SILAC-based protein identification (CLASPI) approach can be used to profile protein-protein interactions mediated by PTMs, such as lysine methylation.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Cells, Cultured
  • HeLa Cells
  • Histones / chemistry
  • Histones / metabolism
  • Humans
  • Lysine / chemistry
  • Lysine / metabolism
  • Mass Spectrometry
  • Molecular Structure
  • Protein Binding
  • Protein Processing, Post-Translational*
  • Proteins / chemistry*
  • Proteins / metabolism
  • Proteomics*


  • Histones
  • Proteins
  • Lysine