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 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.Protein affinity reagents (PARs), 1 most commonly antibodies, are essential and ubiquitous reagents in academic and From the

Bioanalytical chemistry of cytokines – A review

“…The main driving force for designing these different targets is to allow for a rapid production of much-needed, reproducible, and stable affinity agents to new targets as they are discovered in biomedical research. Such reagents could then be kept in a large database of affinity reagents that would include both antibodies and aptamers for use in different proteomics applications [165]. There have been new aptamers made to different cytokine proteins with detection limits reported in the 10 fM range for IL-6 (1.4 pg/mL) and VEGF (0.27 pg/mL) [166].…”

Use of micro-emulsion technology for the directed evolution of antibodies

“…Through the use of appropriate counter-selection steps, it is possible to guide recognition of new epitopes or discriminate between certain molecular features of a target (i.e., conformation, post-translational modification). Thus, there has been a great deal of recent interest in tapping the potential of recombinant affinity reagents for characterizing the human proteome [1][2][3][4][5], and the early comparisons to traditional antibodies are promising [6,7]. Furthermore, it takes less time to identify a recombinant affinity reagent to a target than to generate a rabbit polyclonal or mouse monoclonal antibody [8], and one can do some experiments that are impossible with traditional antibodies, such as evolve higher affinities [9,10], express inside cells and perturb targets [11,12], mislocalize targets in embryos [13], create biosensors [14], and incorporate unnatural amino acids for chemical derivatization [15], which allows new labeling, capturing and immobilization approaches.…”

High-content affinity-based proteomics: unlocking protein biomarker discovery

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