Mapping protein-protein interactions by quantitative proteomics

Methods Mol Biol. 2010;658:267-78. doi: 10.1007/978-1-60761-780-8_16.

Abstract

Proteins exert their function inside a cell generally in multiprotein complexes. These complexes are highly dynamic structures changing their composition over time and cell state. The same protein may thereby fulfill different functions depending on its binding partners. Quantitative mass spectrometry (MS)-based proteomics in combination with affinity purification protocols has become the method of choice to map and track the dynamic changes in protein-protein interactions, including the ones occurring during cellular signaling events. Different quantitative MS strategies have been used to characterize protein interaction networks. In this chapter we describe in detail the use of stable isotope labeling by amino acids in cell culture (SILAC) for the quantitative analysis of stimulus-dependent dynamic protein interactions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / chemistry
  • Cell Extracts / chemistry
  • Chromatography, Liquid
  • Electrophoresis, Polyacrylamide Gel
  • HeLa Cells
  • Humans
  • Immunoprecipitation
  • Isotope Labeling
  • Protein Binding
  • Proteins / chemistry
  • Proteins / isolation & purification
  • Proteins / metabolism*
  • Proteomics / methods*
  • Signal Transduction
  • Tandem Mass Spectrometry

Substances

  • Amino Acids
  • Cell Extracts
  • Proteins