@article{132261,
  keywords = {Proteins, Humans, proteomics, Mass Spectrometry, Protein Interaction Mapping, Chromatography, Affinity, Databases, Factual},
  author = {Dattatreya Mellacheruvu and Zachary Wright and Amber Couzens and Jean-Philippe Lambert and Nicole St-Denis and Tuo Li and Yana Miteva and Simon Hauri and Mihaela Sardiu and Teck Yew Low and Vincentius Halim and Richard Bagshaw and Nina Hubner and Abdallah Al-Hakim and Annie Bouchard and Denis Faubert and Damian Fermin and Wade Dunham and Marilyn Goudreault and Zhen-Yuan Lin and Beatriz Gonzalez Badillo and Tony Pawson and Daniel Durocher and Benoit Coulombe and Ruedi Aebersold and Giulio Superti-Furga and Jacques Colinge and Albert Heck and Hyungwon Choi and Matthias Gstaiger and Shabaz Mohammed and Ileana Cristea and Keiryn Bennett and Mike Washburn and Brian Raught and Rob Ewing and Anne-Claude Gingras and Alexey Nesvizhskii},
  title = {The CRAPome: a contaminant repository for affinity purification-mass spectrometry data},
  abstract = {<p>Affinity purification coupled with mass spectrometry (AP-MS) is 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 (for example, proteins that interact with the solid-phase support, affinity reagent or epitope tag) is a challenging task. The standard approach is to identify nonspecific interactions using one or more negative-control purifications, but many small-scale AP-MS studies do not capture a complete, accurate background protein set when available controls are limited. 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 its use for scoring protein-protein interactions. The repository (currently available for Homo sapiens and Saccharomyces cerevisiae) and computational tools are freely accessible at http://www.crapome.org/.</p>
},
  year = {2013},
  journal = {Nat Methods},
  volume = {10},
  pages = {730-6},
  month = {08/2013},
  issn = {1548-7105},
  doi = {10.1038/nmeth.2557},
  language = {eng},
}