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.

1. Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, Ontario M5S 3E1, Canada
2. Department of Medical Genetics and Microbiology, University of Toronto, 1 Kings College Circle, Toronto, Ontario M5S 1A8, Canada
3. Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
4. Department of Molecular Biophysics and Biochemistry, 266 Whitney Avenue, Yale University, PO Box 208114, New Haven, Connecticut 06520, USA
5. Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M4K 1X8, Canada
6. Affinium Pharmaceuticals, 100 University Avenue, Toronto, Ontario M5J 1V6, Canada
7. Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, UCSF, Genentech Hall S472C, 600 16th St, San Francisco, California 94143, USA
8. Comparative Genomics Laboratory, Nara Institute of Science and Technology 8916-5, Takayama, Ikoma, Nara 630-0101, Japan
9. Department of Biochemistry, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St Louis, Missouri 63104, USA
10. Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA
11. †Present address: Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, California 94143, USA
12. *These authors contributed equally to this work

Correspondence to: Andrew Emili^1,2Jack F. Greenblatt^1,2 Correspondence and requests for materials should be addressed to J.F.G (Email: jack.Greenblatt@utoronto.ca) or A.E. (Email: Andrew.emili@utoronto.ca). Protein interaction information from this paper has been provided to the BioGRID database (http://thebiogrid.org), as well as the International Molecular Interaction Exchange consortium (IMEx, http://imex.sf.net) consisting of BIND, DIP, IntAct, MINT and Mpact (MIPS).

Received 20 December 2005 | Accepted 23 February 2006 |

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