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Standardizing antibody validation data | Top Antibody Feature of 2010

02/02/2010
Aleszu Bajak

An international consortium envisions an online antibody warehouse where researchers can compare protein affinity reagents. The problem is that there’s no standardized format for the data.

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The foremost goal of biomedical research today is to understand the genetic basis of human disease. Protein affinity reagents (PARs)—most commonly antibodies—are essential in these research efforts. For decades, standard laboratory techniques have relied on PARs to detect, purify, image, and characterize proteins.

Although many laboratories use PARs on a daily basis, these reagents may not be standardized or validated to ensure quality control and avoid misinterpretation of generated data. Indeed, a 2008 study on more than 5,000 antibodies from over 50 commercial providers, conducted at the Royal Institute of Technology in Stockholm, Sweden, found that nearly half (49%) of the tested antibodies failed to function or their staining patterns were inconsistent with the previous literature or bioinformatics reports (1) .

Immunofluorescent staining of human U-251MG cell line using an antibody HPA011555 towards protein GOGB1. Source: AntibodypediA
“The antibodies you get today are not always comparable and essential data are not defined,” says Stefan Dübel, director of the department of biotechnology at the Technical University of Braunschweig in Germany. Antibodies that don’t bind or stain consistently pose a huge problem for biomedical researchers, while cross-reactivity or improper binding can potentially stall experiments for weeks or even years. According to Dübel, new virtual antibody resources with publicly available validation data would help researchers circumvent these problems. “It will allow you to find antibodies that have been validated in the assay you want to do,” Dübel told BioTechniques.

In the Jan. 10, 2010 issue of Molecular and Cellular Proteomics, Dübel and his colleagues in the European ProteomeBinders consortium—which includes the Swedish Human Protein Resource, the German Antibody Factory, and 22 other leading academic and commercial laboratories—published a study titled “Report: A community standard format for the representation of protein affinity reagents,” which envisions such an online antibody warehouse where all available affinity reagents from different providers could be catalogued along with documentation comparing cost and quality.

Dübel and his colleagues do face a major hurdle when it comes to the success of such a resource: at present there is no standard format for PAR validation data. As a first step toward a comprehensive and accessible database, the authors of the study have devised an XML-based standard format that categorizes affinity reagents and lists all experimental data and antibody attributes. The proposed Proteomics Standards Initiative (PSI)-PAR standard was built on a mature proteomics data format, the PSI-molecular interaction (MI) standard, a widely accepted and established standard for molecular interaction data. The adoption of the PSI-PAR standard would allow researchers to compare, exchange, and verify PAR validation data.

There are already plans for the integration of the PSI-PAR format. In Sept. 2008, the ProteomeBinders program and the Human Proteome Organization’s Human Antibody Initiative launched the AntibodypediA database (2), which will soon adopt the XML-based PSI-PAR data standard. The database provides application-specific validation scores on publicly available antibodies with corresponding experimental validation data. Users can provide feedback and comments on the use of each antibody in the database. AntibodypediA currently contains over 7100 reviewed binders and validation data from over 21,000 experiments. A fourth version released in Jan. 2010 introduced batch submission, provider-supported applications, and simplified the layout.

But Dübel’s and his colleagues’ vision of an online antibody warehouse is slightly different from AntibodypediA. In their vision, researchers would be able to compare the cost, quality, and application-specific validation data of antibodies, view protocols, and purchase the appropriate antibodies for their needs.

It remains to be seen whether AntibodypediA will grow into the antibody warehouse envisioned by the European ProteomeBinders consortium or if researchers will create an entirely new resource. Either way, Dübel and his colleagues believe that the recently published PSI-PAR standard format will perpetuate standardized antibody validation data, expedite biomedical research, and foster an international collaborative effort on research into the proteome.

References

1. Berglund , L. 2008. A genecentric human protein atlas for expression profiles based on antibodies. Mol. Cell Proteomics. 7:2019-2027.

2. Björling E., and M. Uhlén. 2008. AntibodypediA - a portal for sharing antibody and antigen validation data. Mol Cell Proteomics. 7:2028-2037.

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2010 marked the beginning of our Methods-specific Newsletter series. Covering cell culture, microscopy, PCR, and antibody technology, BioTechniques brought you the latest methodological and technical advances in these exciting fields through weekly feature articles and news stories. If you enjoyed the Top Antibody Feature of 2010, check out the rest of the editors’ picks of our favorite methods-specific news features from 2010 here.