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.
Highlights
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
This study describes the production of three monoclonal antibodies and design of a capture antigen detection ELISA intended to be used as diagnostic tools for the human group B rotavirus, an agent implicated in epidemic outbreaks of diarrhea in China
We have provided the first framework for a common representation of protein affinity reagents, a very complex domain of proteomics, spanning a range of biological and chemical entities and numerous experimental techniques on a proteome-wide scale
Summary
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. Many of the existing PARs have not been adequately validated with regard to epitope site, specificity, affinity for different protein forms (splice variants and native/denatured form) or applicability in experimental techniques (e.g. immunohistochemistry versus Western blot). This hampers rational choices by PAR users who lose time and money if purchased affinity reagent proves inadequate for their needs. The Swedish Human Protein Atlas [4, 5] catalogues protein distribution in healthy and diseased tissues and subcellular localization data in various cell types For this purpose monospecific antibodies (affinity-purified polyclonal antibodies) are manufactured, quality-controlled, and applied in house. Array- and bead-based systems are applied in selection protocols optimized toward minimum body; xref, cross-reference; HSA, human serum albumin; DARPin, designed ankyrin repeat protein; Her, human epidermal growth factor receptor 2
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