A community standard format for the representation of protein affinity reagents

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 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.

Fig. 1.

Use cases for HUPO PSI-PAR format. Each data exchange or sharing event is illustrated with an arrow in the diagram. The common means of PAR representation facilitate the building of integrated networks of PAR-producing and -characterizing centers, here exemplified by ProteomeBinders. This will be of tremendous benefit for the scientific community as it allows for centralized and standardized sources of information on quality and availability of PARs (“Public Warehouse of Affinity Reagents” in the figure).

Fig. 2.

Graphical representation of PSI-MI XML2.5 schema. Some elements have been collapsed for clarity (indicated by a “+” in a rectangular box). The figure is derived from the publication of the PSI-MI 2.5 format (14).

Fig. 3.

Representative section of PSI-PAR controlled vocabulary displayed in Ontology Lookup Service (16). The two new CV subtypes “experimental scope” and “molecule production method” can be seen at the bottom.