The Contaminant Repository for Affinity Purification (CRAPome) is a resource for the analysis of interaction proteomics data. Supported by the repository of negative control affinity purifications, the CRAPome enables the users to search for a specific protein or browse frequent fliers lists.Importantly, the CRAPome also offers an intuitive interface to a number of analytical tools such as SAINT, CompPASS-like scoring, and simple fold change enrichment scoring functions to enable users to analyze their data using their own negative control data or supplement these controls with selected controls from the CRAPome repository.

While affinity purification coupled with mass spectrometry (AP-MS) is widely used for the identification of protein-protein interactions, determining which of the identified polypeptides represent bona fide interactors versus those that are background contaminants (e.g. proteins that interact with the solid-phase support, affinity reagent orepitope tag) is a challenging task. While nonspecific interactions can be identified by computationally comparing AP-MS data for a given bait to one or more negative controls, many small-scale AP-MS studies do not capture a complete, accurate background protein set. Since negative controls are largely bait-independent, aggregating negative controls from multiple AP-MS studies can increase coverage and improve the characterization of background associated with a given experimental protocol. In the CRAPome, negative control experiments generated by research groups across the world are collected (raw mass spectrometry data), reprocessed using a common pipeline, and annotated (e.g. species, cell line, epitope tag, affinity matrix, etc.). This enables organization of the data to facilitate selection of controls that most resemble the experimental conditions defined by a user.

Contaminant Repository for Affinity Purification is a collaboration between Alexey Nesvizhskii and Anne-Claude Gingras Labs.
The CRAPome: a Contaminant Repository for Affinity Purification Mass Spectrometry Data.

D Mellacheruvu, Z Wright, A Couzens, J Lambert, N St-Denis, T Li, Y Miteva, S Hauri, M Sardiu, T Low, V Halim, R Bagshaw, N Hubner, A Hakim, A Bouchard, D Faubert, D Fermin, W Dunham, M Goudreault, Z Lin, B Badillo, T Pawson, D Durocher, B Coulombe, R Aebersold, G Furga, Jacques Colinge, A Heck, H Choi, M Gstaiger, S Mohammed, I Cristea, K Bennett, M Washburn, B Raught, R Ewing, AC Gingras, A Nesvizhskii. Nature Methods 10, 730–736 (2013) doi:10.1038/nmeth.2557 .

For all inquiries, please contact:

Alexey Nesvizhskii
University of Michigan, Ann Arbor
email: nesvi@umich.edu

Anne-Claude Gingras
Samuel Lunenfeld Research Institute, Toronto
email: gingras@lunenfeld.ca