Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

Nevan J. Krogan, Gerard Cagney, Haiyuan Yu, Gouqing Zhong, Xinghua Guo, Alexandr Ignatchenko, Joyce Li, Shuye Pu, Nira Datta, Aaron P. Tikuisis, Thanuja Punna, José M. Peregrín-Alvarez, Michael Shales, Xin Zhang, Michael Davey, Mark D. Robinson, Alberto Paccanaro, James E. Bray, Anthony Sheung, Bryan Beattie, Dawn P. Richards, Veronica Canadien, Atanas Lalev, Frank Mena, Peter Wong, Andrei Starostine, Myra M. Canete, James Vlasblom, Samuel Wu, Chris Orsi, Sean R. Collins, Shamanta Chandran, Robin Haw, Jennifer J. Rilstone, Kiran Gandi, Natalie J. Thompson, Gabe Musso, Peter St Onge, Shaun Ghanny, Mandy H. Y. Lam, Gareth Butland, Amin M. Altaf-Ul, Shigehiko Kanaya, Ali Shilatifard, Erin O'Shea, Jonathan S. Weissman, C. James Ingles, Timothy R. Hughes, John Parkinson, Mark Gerstein, Shoshana J. Wodak, Andrew Emili () and Jack F. Greenblatt ()
Additional contact information
Nevan J. Krogan: University of Toronto
Gerard Cagney: University of Toronto
Haiyuan Yu: Yale University
Gouqing Zhong: University of Toronto
Xinghua Guo: University of Toronto
Alexandr Ignatchenko: University of Toronto
Joyce Li: University of Toronto
Shuye Pu: Hospital for Sick Children
Nira Datta: University of Toronto
Aaron P. Tikuisis: University of Toronto
Thanuja Punna: University of Toronto
José M. Peregrín-Alvarez: Hospital for Sick Children
Michael Shales: University of Toronto
Xin Zhang: University of Toronto
Michael Davey: University of Toronto
Mark D. Robinson: University of Toronto
Alberto Paccanaro: Yale University
James E. Bray: University of Toronto
Anthony Sheung: University of Toronto
Bryan Beattie: Affinium Pharmaceuticals
Dawn P. Richards: Affinium Pharmaceuticals
Veronica Canadien: Affinium Pharmaceuticals
Atanas Lalev: University of Toronto
Frank Mena: Affinium Pharmaceuticals
Peter Wong: University of Toronto
Andrei Starostine: University of Toronto
Myra M. Canete: University of Toronto
James Vlasblom: Hospital for Sick Children
Samuel Wu: Hospital for Sick Children
Chris Orsi: Hospital for Sick Children
Sean R. Collins: UCSF
Shamanta Chandran: University of Toronto
Robin Haw: University of Toronto
Jennifer J. Rilstone: University of Toronto
Kiran Gandi: University of Toronto
Natalie J. Thompson: University of Toronto
Gabe Musso: University of Toronto
Peter St Onge: University of Toronto
Shaun Ghanny: University of Toronto
Mandy H. Y. Lam: University of Toronto
Gareth Butland: University of Toronto
Amin M. Altaf-Ul: Nara Institute of Science and Technology 8916-5
Shigehiko Kanaya: Nara Institute of Science and Technology 8916-5
Ali Shilatifard: Saint Louis University School of Medicine
Erin O'Shea: Harvard University
Jonathan S. Weissman: UCSF
C. James Ingles: University of Toronto
Timothy R. Hughes: University of Toronto
John Parkinson: Hospital for Sick Children
Mark Gerstein: Yale University
Shoshana J. Wodak: Hospital for Sick Children
Andrew Emili: University of Toronto
Jack F. Greenblatt: University of Toronto

Nature, 2006, vol. 440, issue 7084, 637-643

Abstract: Abstract Identification of protein–protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ionization–time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein–protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein–protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.

Date: 2006
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DOI: 10.1038/nature04670

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