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Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

Abstract

The recent abundance of genome sequence data has brought an urgent need for systematic proteomics to decipher the encoded protein networks that dictate cellular function1. 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 expression2,3,4. With the advent of ultrasensitive mass spectrometric protein identification methods, it is feasible to identify directly protein complexes on a proteome-wide scale5,6. 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 studies3,4. 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.

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Figure 1: Two kinase-based signalling networks.
Figure 2: The DNA damage response network.
Figure 3: Comparison of large-scale protein interaction networks with interactions reported in the literature.

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Acknowledgements

We thank J. Chen, B. Kuehl, H. Li, V. Lay, B. Tuekam, S. Zhang, M. Patel, P. O'Donnell, I. Dutschek, U. Friedrich, M. Hansen, J. Brønd, H. Lieu, R. Woolstencroft, L. Harrington, F. Sicheri, A. Breitkreutz, C. Boone, B. Andrews and T. Hughes for discussions and/or technical assistance. This work was supported in part by grants from the Canadian Institutes of Health Research (CIHR), the Ontario Research and Development Challenge Fund and MDS-Sciex to T.P., D.D., C.H. and M.T. T.P. is a Distinguished Scientist of the CIHR; M.F.M. is a CIHR Scientist; D.D. is a Canada Research Chair in Proteomics, Bioinformatics and Functional Genomics and a Hitchings-Elion fellow of the Burroughs-Wellcome Fund; and M.T. is a Canada Research Chair in Biochemistry.

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Correspondence to Daniel Figeys.

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Ho, Y., Gruhler, A., Heilbut, A. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180–183 (2002). https://doi.org/10.1038/415180a

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