Dattatreya Mellacheruvu 1 , 2 , Zachary Wright 2 , Amber L. Couzens 3 , Jean-Philippe Lambert 3 , Nicole St-Denis 3 , Tuo Li 4 , Yana V. Miteva 4 , Simon Hauri 5 , Mihaela E. Sardiu 6 , Teck Yew Low 7 , 8 , Vincentius A. Halim 7 , 8 , 9 , Richard D. Bagshaw 3 , Nina C. Hubner 10 , Abdallah al-Hakim 3 , Annie Bouchard 11 , Denis Faubert 11 , Damian Fermin 1 , Wade H. Dunham 3 , 12 , Marilyn Goudreault 3 , Zhen-Yuan Lin 3 , Beatriz Gonzalez Badillo 3 , Tony Pawson 3 , 12 , Daniel Durocher 3 , 12 , Benoit Coulombe 11 , 13 , Ruedi Aebersold 5 , Giulio Superti-Furga 14 , Jacques Colinge 14 , Albert J. R. Heck 7 , 8 , Hyungwon Choi 15 , Matthias Gstaiger 5 , Shabaz Mohammed 7 , 8 , Ileana M. Cristea 4 , Keiryn L. Bennett 14 , Mike P. Washburn 6 , 16 , Brian Raught 17 , 18 , Rob M. Ewing 19 , 20 , Anne-Claude Gingras 3 , 12 , Alexey I. Nesvizhskii 1 , 2
07 July 2013
Affinity purification coupled with mass spectrometry (AP-MS) is now a widely used approach for the identification of protein-protein interactions. However, for any given protein of interest, determining which of the identified polypeptides represent bona fide interactors versus those that are background contaminants ( e.g. proteins that interact with the solid-phase support, affinity reagent or epitope tag) is a challenging task. While the standard approach is to identify nonspecific interactions using one or more negative controls, most small-scale AP-MS studies do not capture a complete, accurate background protein set. Fortunately, negative controls are largely bait-independent. Hence, aggregating negative controls from multiple AP-MS studies can increase coverage and improve the characterization of background associated with a given experimental protocol. Here we present the Contaminant Repository for Affinity Purification (the CRAPome) and describe the use of this resource to score protein-protein interactions. The repository (currently available for Homo sapiens and Saccharomyces cerevisiae) and computational tools are freely available online at www.crapome.org.