The CRAPome: a Contaminant Repository for Affinity Purification Mass Spectrometry Data

By Dattatreya Mellacheruvu, Zachary Wright, Amber L. Couzens, Jean-Philippe Lambert, N. St-Denis, Tuo Li, Y. Miteva, Simon Hauri, Mihaela E. Sardiu, T. Low and 28 more. Nature Methods, 2013

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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/.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/18ead0eeec14b71215bc2d8062f26b01eab973c4

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Citations in the corpus

SAINTexpress: improvements and additional features in Significance Analysis of Interactome software (2013, methodology): “The fold change was also found to be a useful summary in the recent report describing the scoring of protein interactions using tools implemented as a part of the CRAPome resource (FC scores) [8].”
Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites. (2014, methodology): “After filtering out background contaminants using the CRAPOME database (Mellacheruvu et al., 2013) (Experimental Procedures), one of the most enriched proteins was WTAP, the human ortholog of Mum2, a crucial component of the yeast methyltransferase complex (Agarwala et al.”
Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes (2016, background): “org) (18)—such as cytoskeleton and heat-shock proteins, elongation factors, and histones—some of the F5-100K-enriched proteins were recovered in the IgG-PD: MVP, hornerin, complement C3, and serum albumin.”