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The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.


ABSTRACT: 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/.

SUBMITTER: Mellacheruvu D 

PROVIDER: S-EPMC3773500 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature

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The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.

Mellacheruvu Dattatreya D   Wright Zachary Z   Couzens Amber L AL   Lambert Jean-Philippe JP   St-Denis Nicole A NA   Li Tuo T   Miteva Yana V YV   Hauri Simon S   Sardiu Mihaela E ME   Low Teck Yew TY   Halim Vincentius A VA   Bagshaw Richard D RD   Hubner Nina C NC   Al-Hakim Abdallah A   Bouchard Annie A   Faubert Denis D   Fermin Damian D   Dunham Wade H WH   Goudreault Marilyn M   Lin Zhen-Yuan ZY   Badillo Beatriz Gonzalez BG   Pawson Tony T   Durocher Daniel D   Coulombe Benoit B   Aebersold Ruedi R   Superti-Furga Giulio G   Colinge Jacques J   Heck Albert J R AJ   Choi Hyungwon H   Gstaiger Matthias M   Mohammed Shabaz S   Cristea Ileana M IM   Bennett Keiryn L KL   Washburn Mike P MP   Raught Brian B   Ewing Rob M RM   Ewing Rob M RM   Gingras Anne-Claude AC   Nesvizhskii Alexey I AI  

Nature methods 20130707 8


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 u  ...[more]

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