title: Deciphering protein complexes and protein interaction networks by tandem affinity purification and mass spectrometry: analytical perspective.
abstract: We employed a combination of tandem affinity purification and mass spectrometry for deciphering protein complexes and the protein interaction network in budding yeast. 53 genes were epitope-tagged, and their interaction partners were isolated by two-step immunoaffinity chromatography from whole cell lysates. 38 baits pulled down a total of 220 interaction partners, which are members of 19 functionally distinct protein complexes. We identified four proteins shared between complexes of different functionality thus charting segments of a protein interaction network. Concordance with the results of genome-wide two-hybrid screening was poor (14% of identified interactors overlapped) suggesting that the two approaches may provide complementary views on physical interactions within the proteome.
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics (MPI CBG), Pfotenhauerstrasse 108, 01307 Dresden, Germany.
authors.forename: Anna
authors.initials: A
authors.lastname: Shevchenko
authors.forename: Daniel
authors.initials: D
authors.lastname: Schaft
authors.forename: Assen
authors.initials: A
authors.lastname: Roguev
authors.forename: W W M Pim
authors.initials: WW
authors.lastname: Pijnappel
authors.forename: A Francis
authors.initials: AF
authors.lastname: Stewart
authors.forename: Andrej
authors.initials: A
authors.lastname: Shevchenko
mesh_terms: D002846:Chromatography, Affinity / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D010449:Peptide Mapping / Q000379:methods; D020543:Proteome / Q000235:genetics / Q000302:isolation & purification*; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000302:isolation & purification; D020798:Two-Hybrid System Techniques
chemical_list: D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins