Affinity proteomics to study endogenous protein complexes: pointers, pitfalls, preferences and perspectives

Biotechniques. 2015 Mar 1;58(3):103-19. doi: 10.2144/000114262. eCollection 2015 Mar.


Dissecting and studying cellular systems requires the ability to specifically isolate distinct proteins along with the co-assembled constituents of their associated complexes. Affinity capture techniques leverage high affinity, high specificity reagents to target and capture proteins of interest along with specifically associated proteins from cell extracts. Affinity capture coupled to mass spectrometry (MS)-based proteomic analyses has enabled the isolation and characterization of a wide range of endogenous protein complexes. Here, we outline effective procedures for the affinity capture of protein complexes, highlighting best practices and common pitfalls.

Keywords: affinity; interactomics; protein complex; protein purification; proteomics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatography, Affinity / methods*
  • Humans
  • Mass Spectrometry
  • Multiprotein Complexes / chemistry
  • Multiprotein Complexes / isolation & purification*
  • Protein Binding
  • Proteins / chemistry
  • Proteins / isolation & purification*
  • Proteomics*


  • Multiprotein Complexes
  • Proteins