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

Rob M. Ewing, Peter Chu, Fred Elisma, Hongyan Li, Paul Taylor, Shane Climie, Linda McBroom-Cerajewski, Mark D. Robinson, Liam O'Connor, Michael Li, Rod Taylor, Moyez Dharsee, Yuen Ho, Adrian Heilbut, Lynda Moore, Shudong Zhang, Olga Ornatsky, Yury V. Bukhman, Martin Ethier, Yinglun ShengJulian Vasilescu, Mohamed Abu-Farha, Jean Philippe Lambert, Henry S. Duewel, Ian I. Stewart, Bonnie Kuehl, Kelly Hogue, Karen Colwill, Katharine Gladwish, Brenda Muskat, Robert Kinach, Sally Lin Adams, Michael F. Moran, Gregg B. Morin, Thodoros Topaloglou, Daniel Figeys

Research output: Contribution to journalArticlepeer-review

687 Citations (Scopus)


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.

Original languageEnglish
Article number89
JournalMolecular Systems Biology
Publication statusPublished - 21 Mar 2007


  • Human interactome
  • Protein-protein interaction


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