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 BeattieDawn 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, Jack F. Greenblatt

Research output: Contribution to journalArticle

2047 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)637-643
Number of pages7
JournalNature
Volume440
Issue number7084
DOIs
StatePublished - Mar 30 2006

ASJC Scopus subject areas

  • General

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    Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A. P., Punna, T., Peregrín-Alvarez, J. M., Shales, M., Zhang, X., Davey, M., Robinson, M. D., Paccanaro, A., Bray, J. E., Sheung, A., ... Greenblatt, J. F. (2006). Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440(7084), 637-643. https://doi.org/10.1038/nature04670