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

Dattatreya Mellacheruvu, Zachary Wright, Amber L. Couzens, Jean Philippe Lambert, Nicole A. St-Denis, Tuo Li, Yana V. Miteva, Simon Hauri, Mihaela E. Sardiu, Low Teck Yew, Vincentius A. Halim, Richard D. Bagshaw, Nina C. Hubner, Abdallah Al-Hakim, Annie Bouchard, Denis Faubert, Damian Fermin, Wade H. Dunham, Marilyn Goudreault, Zhen Yuan LinBeatriz Gonzalez Badillo, Tony Pawson, Daniel Durocher, Benoit Coulombe, Ruedi Aebersold, Giulio Superti-Furga, Jacques Colinge, Albert J R Heck, Hyungwon Choi, Matthias Gstaiger, Shabaz Mohammed, Ileana M. Cristea, Keiryn L. Bennett, Mike P. Washburn, Brian Raught, Rob M. Ewing, Anne Claude Gingras, Alexey I. Nesvizhskii

Research output: Contribution to journalArticle

506 Citations (Scopus)

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/.

Original languageEnglish
Pages (from-to)730-736
Number of pages7
JournalNature Methods
Volume10
Issue number8
DOIs
Publication statusPublished - 1 Aug 2013
Externally publishedYes

Fingerprint

Purification
Mass spectrometry
Mass Spectrometry
Impurities
Proteins
Yeast
Saccharomyces cerevisiae
Epitopes
Peptides

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Biochemistry
  • Cell Biology

Cite this

Mellacheruvu, D., Wright, Z., Couzens, A. L., Lambert, J. P., St-Denis, N. A., Li, T., ... Nesvizhskii, A. I. (2013). The CRAPome: A contaminant repository for affinity purification-mass spectrometry data. Nature Methods, 10(8), 730-736. https://doi.org/10.1038/nmeth.2557

The CRAPome : A contaminant repository for affinity purification-mass spectrometry data. / Mellacheruvu, Dattatreya; Wright, Zachary; Couzens, Amber L.; Lambert, Jean Philippe; St-Denis, Nicole A.; Li, Tuo; Miteva, Yana V.; Hauri, Simon; Sardiu, Mihaela E.; Teck Yew, Low; Halim, Vincentius A.; Bagshaw, Richard D.; Hubner, Nina C.; Al-Hakim, Abdallah; Bouchard, Annie; Faubert, Denis; Fermin, Damian; Dunham, Wade H.; Goudreault, Marilyn; Lin, Zhen Yuan; Badillo, Beatriz Gonzalez; Pawson, Tony; Durocher, Daniel; Coulombe, Benoit; Aebersold, Ruedi; Superti-Furga, Giulio; Colinge, Jacques; Heck, Albert J R; Choi, Hyungwon; Gstaiger, Matthias; Mohammed, Shabaz; Cristea, Ileana M.; Bennett, Keiryn L.; Washburn, Mike P.; Raught, Brian; Ewing, Rob M.; Gingras, Anne Claude; Nesvizhskii, Alexey I.

In: Nature Methods, Vol. 10, No. 8, 01.08.2013, p. 730-736.

Research output: Contribution to journalArticle

Mellacheruvu, D, Wright, Z, Couzens, AL, Lambert, JP, St-Denis, NA, Li, T, Miteva, YV, Hauri, S, Sardiu, ME, Teck Yew, L, Halim, VA, Bagshaw, RD, Hubner, NC, Al-Hakim, A, Bouchard, A, Faubert, D, Fermin, D, Dunham, WH, Goudreault, M, Lin, ZY, Badillo, BG, Pawson, T, Durocher, D, Coulombe, B, Aebersold, R, Superti-Furga, G, Colinge, J, Heck, AJR, Choi, H, Gstaiger, M, Mohammed, S, Cristea, IM, Bennett, KL, Washburn, MP, Raught, B, Ewing, RM, Gingras, AC & Nesvizhskii, AI 2013, 'The CRAPome: A contaminant repository for affinity purification-mass spectrometry data', Nature Methods, vol. 10, no. 8, pp. 730-736. https://doi.org/10.1038/nmeth.2557
Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis NA, Li T et al. The CRAPome: A contaminant repository for affinity purification-mass spectrometry data. Nature Methods. 2013 Aug 1;10(8):730-736. https://doi.org/10.1038/nmeth.2557
Mellacheruvu, Dattatreya ; Wright, Zachary ; Couzens, Amber L. ; Lambert, Jean Philippe ; St-Denis, Nicole A. ; Li, Tuo ; Miteva, Yana V. ; Hauri, Simon ; Sardiu, Mihaela E. ; Teck Yew, Low ; Halim, Vincentius A. ; Bagshaw, Richard D. ; Hubner, Nina C. ; Al-Hakim, Abdallah ; Bouchard, Annie ; Faubert, Denis ; Fermin, Damian ; Dunham, Wade H. ; Goudreault, Marilyn ; Lin, Zhen Yuan ; Badillo, Beatriz Gonzalez ; Pawson, Tony ; Durocher, Daniel ; Coulombe, Benoit ; Aebersold, Ruedi ; Superti-Furga, Giulio ; Colinge, Jacques ; Heck, Albert J R ; Choi, Hyungwon ; Gstaiger, Matthias ; Mohammed, Shabaz ; Cristea, Ileana M. ; Bennett, Keiryn L. ; Washburn, Mike P. ; Raught, Brian ; Ewing, Rob M. ; Gingras, Anne Claude ; Nesvizhskii, Alexey I. / The CRAPome : A contaminant repository for affinity purification-mass spectrometry data. In: Nature Methods. 2013 ; Vol. 10, No. 8. pp. 730-736.
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AU - Miteva, Yana V.

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AU - Fermin, Damian

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AU - Goudreault, Marilyn

AU - Lin, Zhen Yuan

AU - Badillo, Beatriz Gonzalez

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AU - Choi, Hyungwon

AU - Gstaiger, Matthias

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AU - Washburn, Mike P.

AU - Raught, Brian

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AU - Gingras, Anne Claude

AU - Nesvizhskii, Alexey I.

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