Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

TitleGlobal landscape of protein complexes in the yeast Saccharomyces cerevisiae.
Publication TypeJournal Article
Year of Publication2006
AuthorsKrogan, 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., Beattie B., Richards D. P., Canadien V., Lalev A., Mena F., Wong P., Starostine A., Canete M. M., Vlasblom J., Wu S., Orsi C., Collins S. R., Chandran S., Haw R., Rilstone J. J., Gandi K., Thompson N. J., Musso G., St Onge P., Ghanny S., H Y Lam M., Butland G., Altaf-Ul A. M., Kanaya S., Shilatifard A., O'Shea E., Weissman J. S., C Ingles J., Hughes T. R., Parkinson J., Gerstein M., Wodak S. J., Emili A., and Greenblatt J. F.
JournalNature
Volume440
Issue7084
Pagination637-43
Date Published2006 Mar 30
ISSN1476-4687
KeywordsBiological Evolution, Conserved Sequence, Mass Spectrometry, Multiprotein Complexes, Protein Binding, Proteome, Proteomics, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins
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.

DOI10.1038/nature04670
Alternate JournalNature
PubMed ID16554755