Advances in protein complex analysis using mass spectrometry

J Physiol. 2005 Feb 15;563(Pt 1):11-21. doi: 10.1113/jphysiol.2004.080440. Epub 2004 Dec 20.


Proteins often function as components of larger complexes to perform a specific function, and formation of these complexes may be regulated. For example, intracellular signalling events often require transient and/or regulated protein-protein interactions for propagation, and protein binding to a specific DNA sequence, RNA molecule or metabolite is often regulated to modulate a particular cellular function. Thus, characterizing protein complexes can offer important insights into protein function. This review describes recent important advances in mass spectrometry (MS)-based techniques for the analysis of protein complexes. Following brief descriptions of how proteins are identified using MS, and general protein complex purification approaches, we address two of the most important issues in these types of studies: specificity and background protein contaminants. Two basic strategies for increasing specificity and decreasing background are presented: whereas (1) tandem affinity purification (TAP) of tagged proteins of interest can dramatically improve the signal-to-noise ratio via the generation of cleaner samples, (2) stable isotopic labelling of proteins may be used to discriminate between contaminants and bona fide binding partners using quantitative MS techniques. Examples, as well as advantages and disadvantages of each approach, are presented.

Publication types

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

MeSH terms

  • Animals
  • Gene Expression Profiling / methods*
  • Humans
  • Mass Spectrometry / methods*
  • Mass Spectrometry / trends
  • Protein Interaction Mapping / methods*
  • Protein Interaction Mapping / trends
  • Proteins / analysis
  • Proteins / chemistry*
  • Proteins / metabolism*
  • Proteomics / methods*
  • Proteomics / trends
  • Sequence Analysis, Protein / methods*
  • Sequence Analysis, Protein / trends


  • Proteins