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; Teck Yew Low; 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 Lin; Beatriz 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

doi:10.1038/nmeth.2557

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

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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, Teck Yew Low, …

Nature methods, Vol.10(8), pp.730-736

01/08/2013

DOI: https://doi.org/10.1038/nmeth.2557

PMID: 23921808

Résumé

631/114/129/2044

631/114/2784

631/1647/2067

631/45/475/2290

Article

Bioinformatics

Biological Microscopy

Biological Techniques

Biomedical Engineering/Biotechnology

Général

Life Sciences

Proteomics

resource

The Contaminant Repository for Affinity Purification (CRAPome) is a database of annotated negative control-data that can be used for filtering out nonspecific interactions in affinity purification-mass spectrometry experiments. 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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Titre: The CRAPome: a contaminant repository for affinity purification–mass spectrometry data
Créateurs - sans rôle: Dattatreya Mellacheruvu - Department of Pathology, University of Michigan, Department of Computational Medicine and Bioinformatics, University of Michigan
Zachary Wright - Department of Computational Medicine and Bioinformatics, University of Michigan
Amber L Couzens - Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital
Jean-Philippe Lambert - Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital
Nicole A St-Denis - Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital
Tuo Li - Department of Molecular Biology, Princeton University
Yana V Miteva - Department of Molecular Biology, Princeton University
Simon Hauri - Department of Biology, Institute of Molecular Systems Biology, ETH Zurich
Mihaela E Sardiu - Stowers Institute for Medical Research
Teck Yew Low - Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Center
Vincentius A Halim - Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Center, Division of Cell Biology, Netherlands Cancer Institute
Richard D Bagshaw - Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital
Nina C Hubner - Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University
Abdallah al-Hakim - Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital
Annie Bouchard - Institut de Recherches Cliniques de Montréal
Denis Faubert - Institut de Recherches Cliniques de Montréal
Damian Fermin - Department of Pathology, University of Michigan
Wade H Dunham - Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto
Marilyn Goudreault - Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital
Zhen-Yuan Lin - Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital
Beatriz Gonzalez Badillo - Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital
Tony Pawson - Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto
Daniel Durocher - Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto
Benoit Coulombe - Institut de Recherches Cliniques de Montréal, Département de Biochimie, Université de Montréal
Ruedi Aebersold - University of Zurich
Giulio Superti-Furga - CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Jacques Colinge - CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Albert J R Heck - Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Center
Hyungwon Choi - Saw Swee Hock School of Public Health, National University of Singapore
Matthias Gstaiger - Department of Biology, Institute of Molecular Systems Biology, ETH Zurich
Shabaz Mohammed - Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Center, Department of Chemistry, University of Oxford, Department of Biochemistry, University of Oxford
Ileana M Cristea - Department of Molecular Biology, Princeton University
Keiryn L Bennett - CeMM Research Center for Molecular Medicine
Mike P Washburn - Stowers Institute for Medical Research, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center
Brian Raught - Ontario Cancer Institute, Department of Medical Biophysics, University of Toronto
Rob M Ewing - Center for Proteomics and Bioinformatics, Case Western Reserve University, Present address: Centre for Biological Sciences, University of Southampton, Southampton, UK
Anne-Claude Gingras - Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto
Alexey I Nesvizhskii - Department of Pathology, University of Michigan, Department of Computational Medicine and Bioinformatics, University of Michigan
Détails de publication: Nature methods, Vol.10(8), pp.730-736
Éditeur: Nature Publishing Group US
Nombre de pages: 7
Identifiants: 99140138009311
Unité académique: Institut de Recherche en Cancérologie de Montpellier - IRCM
Langue: English
Type de ressource: Journal article