Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

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 bina...

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Bibliographic Details
Published in:	Nature (London) Vol. 415; no. 6868; pp. 180 - 183
Main Authors:	Figeys, Daniel, Ho, Yuen, Gruhler, Albrecht, Heilbut, Adrian, Bader, Gary D, Moore, Lynda, Adams, Sally-Lin, Millar, Anna, Taylor, Paul, Bennett, Keiryn, Boutilier, Kelly, Yang, Lingyun, Wolting, Cheryl, Donaldson, Ian, Schandorff, Søren, Shewnarane, Juanita, Vo, Mai, Taggart, Joanne, Goudreault, Marilyn, Muskat, Brenda, Alfarano, Cris, Dewar, Danielle, Lin, Zhen, Michalickova, Katerina, Willems, Andrew R, Sassi, Holly, Nielsen, Peter A, Rasmussen, Karina J, Andersen, Jens R, Johansen, Lene E, Hansen, Lykke H, Jespersen, Hans, Podtelejnikov, Alexandre, Nielsen, Eva, Crawford, Janne, Poulsen, Vibeke, Sørensen, Birgitte D, Matthiesen, Jesper, Hendrickson, Ronald C, Gleeson, Frank, Pawson, Tony, Moran, Michael F, Durocher, Daniel, Mann, Matthias, Hogue, Christopher W. V, Tyers, Mike
Format:	Journal Article
Language:	English
Published:	London Nature Publishing 10-01-2002 Nature Publishing Group
Subjects:	Amino Acid Sequence Baits Biochemistry Biological and medical sciences Cell Cycle Proteins Cloning, Molecular DNA Damage DNA Repair DNA, Fungal Fundamental and applied biological sciences. Psychology high-throughput screening Humans Macromolecular Substances Mass Spectrometry Microbiology Molecular Sequence Data Morphology, structure, chemical composition Mycology Phosphoric Monoester Hydrolases - metabolism Protein Binding Protein Kinases - chemistry Protein Kinases - metabolism Protein-Serine-Threonine Kinases Proteins Proteome proteomes Saccharomyces cerevisiae Saccharomyces cerevisiae - chemistry Saccharomyces cerevisiae Proteins - chemistry Saccharomyces cerevisiae Proteins - isolation & purification Scientific imaging Sequence Alignment Signal Transduction Yeast Yeasts Fungi Characterization Yeast Proteomics Proteome Ascomycetes Molecular complex Method Saccharomyces cerevisiae Mass spectrometry Protein Thallophyta
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Summary:	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.
Bibliography:	ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 ObjectType-Article-1 ObjectType-Feature-2
ISSN:	0028-0836 1476-4687
DOI:	10.1038/415180a