The CRAPome: a contaminant repository for affinity purification–mass spectrometry data
Open accessAbstract
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/.
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Proteome lists were filtered for common mass spectrometry contaminants using a published database.
“all proteome lists were filtered for common mass spectrometry contaminants using a published database42.”
From APOE genotypes differentially remodel the astrocytic lipid droplet proteome to shape lipid droplet dynamics (2026) · cites this paper as [42]
Control selection is essential for judging the specificity of viral-host protein interactions identified.
“The selection of controls is critical for assessing the specificity of the identified viral–host protein interactions.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [27]
Several research groups have put together a resource of AP-MS controls, termed the contaminant repository for affinity purification.
“In an attempt to predict the associations that are likely to be non-specific, several research groups have put together a resource of AP-MS controls, termed the contaminant repository for affinity purification [27].”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [27]
This resource provides useful information about recurring sticky proteins in different cell types or when using certain tags or resins for the isolations.
“This resource provides useful information about recurring sticky proteins in different cell types or when using certain tags or resins for the isolations.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [27]
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Structural insights into IMP2 dimerization and RNA binding
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- Authors
- Mellacheruvu, D., Wright, Z., Couzens, A. L., Lambert, J.-P., St-Denis, N. A., Li, T., Miteva, Y. V., Hauri, S., Sardiu, M. E., Low, T. Y., Halim, V. A., Bagshaw, R. D., Hubner, N. C., al-Hakim, A., Bouchard, A., Faubert, D., Fermin, D., Dunham, W. H., Goudreault, M., Lin, Z.-Y., Badillo, B. G., Pawson, T., Durocher, D., Coulombe, B., Aebersold, R., Superti-Furga, G., Colinge, J., Heck, A. J. R., Choi, H., Gstaiger, M., Mohammed, S., Cristea, I. M., Bennett, K. L., Washburn, M. P., Raught, B., Ewing, R. M., Gingras, A.-C., & Nesvizhskii, A. I.
- Affiliations
- University of Michigan (US)
- Mount Sinai Hospital (CA)
- Princeton University (US)
- ETH Zurich (CH)
- Stowers Institute for Medical Research (US)
- Utrecht University (NL)
- Radboud University Nijmegen (NL)
- Montreal Clinical Research Institute (CA)
- University of Zurich (CH)
- Austrian Academy of Sciences (AT)
- National University of Singapore (SG)
- University of Toronto (CA)
- Case Western Reserve University (US)
- Corresponding author
- Gingras, Anne-Claude
- Nesvizhskii, Alexey I
- ORCID
- Mellacheruvu, Dattatreya
- Couzens, Amber L
- Lambert, Jean-Philippe
- Hauri, Simon
- Sardiu, Mihaela E
- Low, Teck Yew
- Bagshaw, Richard D
- Faubert, Denis
- Fermin, Damian
- Dunham, Wade H
- Durocher, Daniel
- Coulombe, Benoit
- Aebersold, Ruedi
- Colinge, Jacques
- Heck, Albert J R
- Choi, Hyungwon
- Gstaiger, Matthias
- Mohammed, Shabaz
- Cristea, Ileana M
- Bennett, Keiryn L
- Raught, Brian
- Ewing, Rob M
- Gingras, Anne-Claude
- Nesvizhskii, Alexey I
- Venue
- Nature Methods
- Published
- 2013-07-07
- Volume
- 10
- Issue
- 8
- Pages
- 730-736
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC3773500
- OpenAlex
- W2167844024
- Cited by
- 1,686
- References
- 52
- Citations by year
- 2026: 107 · 2025: 119 · 2024: 159 · 2023: 148 · 2022: 180 · 2021: 173 · 2020: 156 · 2019: 141 · 2018: 128 · 2017: 111 · 2016: 103 · 2015: 91 · 2014: 54 · 2013: 14 · 2012: 1
- FWCI
- 39.30
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- ePrints Soton (University of Southampton) (acceptedVersion)
- National University of Singapore (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion)
- Radboud Repository (Radboud University) (submittedVersion)
- Funders
- Canadian Institutes of Health Research (82851_1, MOP 84314)
- National Heart, Lung, and Blood Institute (R01HL112618, HL112618-01)
- National Institute on Drug Abuse (DP1DA026192)
- National Cancer Institute (R21CA160060)
- National Institute of General Medical Sciences (R01GM094231)
- National Institute of Allergy and Infectious Diseases (R21AI102187)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R21HD073044)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Biotin and Related Studies
- Keywords
- affinity purification mass spectrometry, protein-protein interaction, negative control, non-specific interactions, protein-protein interaction network, human, Saccharomyces cerevisiae
- MeSH terms
- Chromatography, Affinity, Humans, Proteins, Mass Spectrometry, Databases, Factual, Protein Interaction Mapping, Proteomics
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