A community standard format for the representation of protein affinity reagents.
Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one on-line warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information and documentation are available on the PSI-PAR web site.
Gloriam
David E
DE
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom. par@psidev.info
Orchard
Sandra
S
Bertinetti
Daniela
D
Björling
Erik
E
Bongcam-Rudloff
Erik
E
Borrebaeck
Carl A K
CA
Bourbeillon
Julie
J
Bradbury
Andrew R M
AR
de Daruvar
Antoine
A
Dübel
Stefan
S
Frank
Ronald
R
Gibson
Toby J
TJ
Gold
Larry
L
Haslam
Niall
N
Herberg
Friedrich W
FW
Hiltke
Tara
T
Hoheisel
Jörg D
JD
Kerrien
Samuel
S
Koegl
Manfred
M
Konthur
Zoltán
Z
Korn
Bernhard
B
Landegren
Ulf
U
Montecchi-Palazzi
Luisa
L
Palcy
Sandrine
S
Rodriguez
Henry
H
Schweinsberg
Sonja
S
Sievert
Volker
V
Stoevesandt
Oda
O
Taussig
Michael J
MJ
Ueffing
Marius
M
Uhlén
Mathias
M
van der Maarel
Silvère
S
Wingren
Christer
C
Woollard
Peter
P
Sherman
David J
DJ
Hermjakob
Henning
H
D003628:Database Management Systems / Q000592:standards; D030562:Databases, Protein / Q000592:standards*; D006801:Humans; D007391:International Cooperation; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods; D009626:Terminology as Topic
D020543:Proteome
Mol Cell Proteomics. 2008 Oct;7(10):2028-37
18667413
Proteomics. 2007 Jul;7(14):2355-7
17570517
Mol Cell Proteomics. 2005 Dec;4(12):1920-32
16127175
Mol Cell Proteomics. 2008 Oct;7(10):2019-27
18669619
BMC Bioinformatics. 2006 Feb 28;7:97
16507094
Nucleic Acids Res. 2007 Jan;35(Database issue):D561-5
17145710
Proteomics. 2007 Aug;7(16):2738-50
17639606
Curr Opin Mol Ther. 2006 Jun;8(3):185-90
16774037
Nat Biotechnol. 2004 Feb;22(2):177-83
14755292
Mol Cell Proteomics. 2006 Oct;5(10):1996-2007
16867976
Nat Methods. 2007 Jan;4(1):13-7
17195019
J Clin Microbiol. 1989 Feb;27(2):245-50
2536755
BMC Biol. 2007 Oct 09;5:44
17925023
Anal Biochem. 2003 Oct 15;321(2):217-25
14511687
Anal Chem. 2008 Apr 1;80(7):2305-10
18456912
Immunol Today. 2000 Aug;21(8):379-82
10916140
J Mol Biol. 2007 Jun 15;369(4):1015-28
17466328
J Biol Chem. 2006 Nov 17;281(46):35167-75
16963452
Proteomics. 2006 Sep;6 Suppl 2:34-8
17031794