Report: 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 large­scale 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 HUPO (Plasma and Liver Proteome Projects) and the U.S. National Cancer Institute (cancer associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality controlled protein­binding 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 facilitate 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 centres and commercial companies all use incompatible formats hindering data exchange. Here we propose PSI­PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI­PAR format is maintained by the HUPO Proteomics Standards Initiative (PSI) and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI­MI, which is a widely accepted and established community standard for molecular interactions data.

Further information and documentation is available on the PSI­PAR web site (http://www.psidev.info/PAR).