Journal
NATURE METHODS
Volume 10, Issue 8, Pages 730-+Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/nmeth.2557
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Funding
- US National Institutes of Health [NIH 5R01GM94231, DP1DA026192, HL112618-01]
- Canadian Institutes of Health Research (CIHR) [MOP-84314, MOP-82851]
- government of Ontario via a Global Leadership Round in Genomics and Life Sciences
- Austrian Academy of Sciences
- Austrian Federal Ministry for Science and Research [820965, 820962]
- European Research Council [ERC-2009-AdG-250179-i-FIVE]
- Austrian Science Fund FWF [P24321-B21, P22282-B11]
- European Molecular Biology Organization long-term fellowship [ATLF463-2008]
- Netherlands Proteomics Center
- European Union [262067]
- Stowers Institute for Medical Research
- Human Frontier Science Program [RGY0079/2009-C]
- Cleveland Foundation
- NIH [1R21 CA16006001A1]
- CIHR
- TD Bank postdoctoral fellowship
- Austrian Science Fund (FWF) [P22282, P24321] Funding Source: Austrian Science Fund (FWF)
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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/.
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