A community standard format for the representation of protein affinity reagents

Research output: Contribution to journalJournal articleResearchpeer-review

  • Sandra Orchard
  • Daniela Bertinetti
  • Erik Björling
  • Erik Bongcam-Rudloff
  • Carl A K Borrebaeck
  • Julie Bourbeillon
  • Andrew R M Bradbury
  • Antoine de Daruvar
  • Stefan Dübel
  • Ronald Frank
  • Toby J Gibson
  • Larry Gold
  • Niall Haslam
  • Friedrich W Herberg
  • Tara Hiltke
  • Jörg D Hoheisel
  • Samuel Kerrien
  • Manfred Koegl
  • Zoltán Konthur
  • Bernhard Korn
  • Ulf Landegren
  • Luisa Montecchi-Palazzi
  • Sandrine Palcy
  • Henry Rodriguez
  • Sonja Schweinsberg
  • Volker Sievert
  • Oda Stoevesandt
  • Michael J Taussig
  • Marius Ueffing
  • Mathias Uhlén
  • Silvère van der Maarel
  • Christer Wingren
  • Peter Woollard
  • David J Sherman
  • Henning Hermjakob
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.
Original languageEnglish
JournalMolecular and Cellular Proteomics
Issue number1
Pages (from-to)1-10
Publication statusPublished - 2010

Bibliographical note

Keywords: Database Management Systems; Databases, Protein; Humans; International Cooperation; Proteome; Proteomics; Terminology as Topic

ID: 21088294