The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.
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/.
Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.
Dattatreya
D
Mellacheruvu
Zachary
Z
Wright
Amber L
AL
Couzens
Jean-Philippe
JP
Lambert
Nicole A
NA
St-Denis
Tuo
T
Li
Yana V
YV
Miteva
Simon
S
Hauri
Mihaela E
ME
Sardiu
Teck Yew
TY
Low
Vincentius A
VA
Halim
Richard D
RD
Bagshaw
Nina C
NC
Hubner
Abdallah
A
Al-Hakim
Annie
A
Bouchard
Denis
D
Faubert
Damian
D
Fermin
Wade H
WH
Dunham
Marilyn
M
Goudreault
Zhen-Yuan
ZY
Lin
Beatriz Gonzalez
BG
Badillo
Tony
T
Pawson
Daniel
D
Durocher
Benoit
B
Coulombe
Ruedi
R
Aebersold
Giulio
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Superti-Furga
Jacques
J
Colinge
Albert J R
AJ
Heck
Hyungwon
H
Choi
Matthias
M
Gstaiger
Shabaz
S
Mohammed
Ileana M
IM
Cristea
Keiryn L
KL
Bennett
Mike P
MP
Washburn
Brian
B
Raught
Rob M
RM
Ewing
Anne-Claude
AC
Gingras
Alexey I
AI
Nesvizhskii
D002846:Chromatography, Affinity / Q000379:methods*; D016208:Databases, Factual; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*
D011506:Proteins