title: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.
abstract: The recent abundance of genome sequence data has brought an urgent need for systematic proteomics to decipher the encoded protein networks that dictate cellular function. To date, generation of large-scale protein-protein interaction maps has relied on the yeast two-hybrid system, which detects binary interactions through activation of reporter gene expression. With the advent of ultrasensitive mass spectrometric protein identification methods, it is feasible to identify directly protein complexes on a proteome-wide scale. Here we report, using the budding yeast Saccharomyces cerevisiae as a test case, an example of this approach, which we term high-throughput mass spectrometric protein complex identification (HMS-PCI). Beginning with 10% of predicted yeast proteins as baits, we detected 3,617 associated proteins covering 25% of the yeast proteome. Numerous protein complexes were identified, including many new interactions in various signalling pathways and in the DNA damage response. Comparison of the HMS-PCI data set with interactions reported in the literature revealed an average threefold higher success rate in detection of known complexes compared with large-scale two-hybrid studies. Given the high degree of connectivity observed in this study, even partial HMS-PCI coverage of complex proteomes, including that of humans, should allow comprehensive identification of cellular networks.
authors.affiliation: MDS Proteomics, 251 Attwell Drive, Toronto, Canada M9W 7H4, and Staermosegaardsvej 6, DK-5230 Odense M, Denmark.
authors.forename: Yuen
authors.initials: Y
authors.lastname: Ho
authors.forename: Albrecht
authors.initials: A
authors.lastname: Gruhler
authors.forename: Adrian
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authors.lastname: Heilbut
authors.forename: Gary D
authors.initials: GD
authors.lastname: Bader
authors.forename: Lynda
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authors.lastname: Moore
authors.forename: Sally-Lin
authors.initials: SL
authors.lastname: Adams
authors.forename: Anna
authors.initials: A
authors.lastname: Millar
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authors.lastname: Taylor
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authors.forename: Lingyun
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authors.lastname: Yang
authors.forename: Cheryl
authors.initials: C
authors.lastname: Wolting
authors.forename: Ian
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authors.lastname: Donaldson
authors.forename: Søren
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authors.lastname: Schandorff
authors.forename: Juanita
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authors.lastname: Shewnarane
authors.forename: Mai
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authors.lastname: Vo
authors.forename: Joanne
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authors.lastname: Taggart
authors.forename: Marilyn
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authors.lastname: Goudreault
authors.forename: Brenda
authors.initials: B
authors.lastname: Muskat
authors.forename: Cris
authors.initials: C
authors.lastname: Alfarano
authors.forename: Danielle
authors.initials: D
authors.lastname: Dewar
authors.forename: Zhen
authors.initials: Z
authors.lastname: Lin
authors.forename: Katerina
authors.initials: K
authors.lastname: Michalickova
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Willems
authors.forename: Holly
authors.initials: H
authors.lastname: Sassi
authors.forename: Peter A
authors.initials: PA
authors.lastname: Nielsen
authors.forename: Karina J
authors.initials: KJ
authors.lastname: Rasmussen
authors.forename: Jens R
authors.initials: JR
authors.lastname: Andersen
authors.forename: Lene E
authors.initials: LE
authors.lastname: Johansen
authors.forename: Lykke H
authors.initials: LH
authors.lastname: Hansen
authors.forename: Hans
authors.initials: H
authors.lastname: Jespersen
authors.forename: Alexandre
authors.initials: A
authors.lastname: Podtelejnikov
authors.forename: Eva
authors.initials: E
authors.lastname: Nielsen
authors.forename: Janne
authors.initials: J
authors.lastname: Crawford
authors.forename: Vibeke
authors.initials: V
authors.lastname: Poulsen
authors.forename: Birgitte D
authors.initials: BD
authors.lastname: Sørensen
authors.forename: Jesper
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authors.lastname: Matthiesen
authors.forename: Ronald C
authors.initials: RC
authors.lastname: Hendrickson
authors.forename: Frank
authors.initials: F
authors.lastname: Gleeson
authors.forename: Tony
authors.initials: T
authors.lastname: Pawson
authors.forename: Michael F
authors.initials: MF
authors.lastname: Moran
authors.forename: Daniel
authors.initials: D
authors.lastname: Durocher
authors.forename: Matthias
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authors.lastname: Mann
authors.forename: Christopher W V
authors.initials: CW
authors.lastname: Hogue
authors.forename: Daniel
authors.initials: D
authors.lastname: Figeys
authors.forename: Mike
authors.initials: M
authors.lastname: Tyers
mesh_terms: D000595:Amino Acid Sequence; D018797:Cell Cycle Proteins; D003001:Cloning, Molecular; D004249:DNA Damage; D004260:DNA Repair; D004271:DNA, Fungal; D006801:Humans; D046911:Macromolecular Substances; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D010744:Phosphoric Monoester Hydrolases / Q000378:metabolism; D011485:Protein Binding; D011494:Protein Kinases / Q000737:chemistry / Q000378:metabolism; D017346:Protein Serine-Threonine Kinases; D020543:Proteome; D012441:Saccharomyces cerevisiae / Q000737:chemistry*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000302:isolation & purification*; D016415:Sequence Alignment; D015398:Signal Transduction
chemical_list: D018797:Cell Cycle Proteins; D004271:DNA, Fungal; D046911:Macromolecular Substances; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D011494:Protein Kinases; C104169:DUN1 protein, S cerevisiae; D017346:Protein Serine-Threonine Kinases; D010744:Phosphoric Monoester Hydrolases