title: Advances in protein complex analysis using mass spectrometry.
abstract: 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.
authors.affiliation: Institute for Systems Biology, Seattle, WA 98103, USA. agingras@systemsbiology.org
authors.forename: Anne-Claude
authors.initials: AC
authors.lastname: Gingras
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Brian
authors.initials: B
authors.lastname: Raught
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods* / Q000639:trends; D025941:Protein Interaction Mapping / Q000379:methods* / Q000639:trends; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000378:metabolism*; D040901:Proteomics / Q000379:methods* / Q000639:trends; D020539:Sequence Analysis, Protein / Q000379:methods* / Q000639:trends
chemical_list: D011506:Proteins