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/.