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A community standard format for the representation of protein affinity reagents

Gloriam, David E.; Orchard, Sandra; Bertinetti, Daniela; Bjorling, Erik; Bongcam-Rudloff, Erik; Borrebaeck, Carl LU ; Bourbeillon, Julie; Bradbury, Andrew R. M.; de Daruvar, Antoine and Duebel, Stefan, et al. (2010) In Molecular & Cellular Proteomics 9(1). p.1-10
Abstract
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... (More)
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 online 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. Molecular & Cellular Proteomics 9: 1-10, 2010. (Less)
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@article{25c324a4-4a75-4f78-9932-660606020f7e,
  abstract     = {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 online 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. Molecular & Cellular Proteomics 9: 1-10, 2010.},
  author       = {Gloriam, David E. and Orchard, Sandra and Bertinetti, Daniela and Bjorling, Erik and Bongcam-Rudloff, Erik and Borrebaeck, Carl and Bourbeillon, Julie and Bradbury, Andrew R. M. and de Daruvar, Antoine and Duebel, Stefan and Frank, Ronald and Gibson, Toby J. and Gold, Larry and Haslam, Niall and Herberg, Friedrich W. and Hiltke, Tara and Hoheisel, Joerg D. and Kerrien, Samuel and Koegl, Manfred and Konthur, Zoltan and Korn, Bernhard and Landegren, Ulf and Montecchi-Palazzi, Luisa and Palcy, Sandrine and Rodriguez, Henry and Schweinsberg, Sonja and Sievert, Volker and Stoevesandt, Oda and Taussig, Michael J. and Ueffing, Marius and Uhlen, Mathias and van der Maarel, Silvere and Wingren, Christer and Woollard, Peter and Sherman, David J. and Hermjakob, Henning},
  issn         = {1535-9484},
  language     = {eng},
  number       = {1},
  pages        = {1--10},
  publisher    = {American Society for Biochemistry and Molecular Biology},
  series       = {Molecular & Cellular Proteomics},
  title        = {A community standard format for the representation of protein affinity reagents},
  url          = {http://dx.doi.org/10.1074/mcp.M900185-MCP200},
  volume       = {9},
  year         = {2010},
}