Wednesday, 19 February 2014

CRAPome - Contaminant Repository for Affinity Purification

Purists might argue that the “ome” stops this being a true acronym but, for me, there can be few finer examples of the art of the contrived acronym than CRAPome - Contaminant Repository for Affinity Purification [for mass spectrometry proeome data]:

Mellacheruvu D et al. (2013). “The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.Nat Methods 10(8): 730-736.

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

Pre hoc genius!