Large-scale mapping of human protein-protein interactions by mass spectrometry

Ewing, Rob M., Chu, Peter, Elisma, Fred, Li, Hongyan, Taylor, Paul, Climie, Shane, McBroom-Cerajewski, Linda, Robinson, Mark D., O'Connor, Liam, Li, Michael, Taylor, Rod, Dharsee, Moyez, Ho, Yuen, Heilbut, Adrian, Moore, Lynda, Zhang, Shudong, Ornatsky, Olga, Bukhman, Yury V, Ethier, Martin, Sheng, Yinglun, Vasilescu, Julian, Abu-Farha, Mohamed, Lambert, Jean-Philippe, Duewel, Henry S., Stewart, Ian I., Kuehl, Bonnie, Hogue, Kelly, Colwill, Karen, Gladwish, Katharine, Muskat, Brenda, Kinach, Robert, Adams, Sally-Lin, Moran, Michael F., Morin, Gregg B., Topaloglou, Thodoros and Figeys, Daniel (2007) Large-scale mapping of human protein-protein interactions by mass spectrometry. Molecular Systems Biology, 3 (89), 89. (doi:10.1038/msb4100134). (PMID:17353931)

Abstract

Mapping protein-protein interactions is an invaluable tool for understanding protein function. Here, we report the first large-scale study of protein-protein interactions in human cells using a mass spectrometry-based approach. The study maps protein interactions for 338 bait proteins that were selected based on known or suspected disease and functional associations. Large-scale immunoprecipitation of Flag-tagged versions of these proteins followed by LC-ESI-MS/MS analysis resulted in the identification of 24,540 potential protein interactions. False positives and redundant hits were filtered out using empirical criteria and a calculated interaction confidence score, producing a data set of 6463 interactions between 2235 distinct proteins. This data set was further cross-validated using previously published and predicted human protein interactions. In-depth mining of the data set shows that it represents a valuable source of novel protein-protein interactions with relevance to human diseases. In addition, via our preliminary analysis, we report many novel protein interactions and pathway associations.

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Contributors

Author: Rob M. Ewing

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