Before using an antibody in an experiment it is essential to validate the antibody for the specific application and sample. Ideally, all this information should be freely available and accessible for every antibody available on the market so that the right antibody can be chosen for the application of interest. To meet this necessity, a database called Antibodypedia (Alm et al., 2014, Bjorling & Uhlen, 2008) has been created. Antibodypedia is a freely available searchable database containing annotated and scored antibodies from commercial and academic providers. The database is organized in a "gene-centric" manner to provide users with an overview of all antibodies available against a particular biomolecule of interest. Since one of the most important tasks of the Antibodypedia portal is to guide antibody users to select an antibody with high reliability, detailed antibody data can be compared using Antibodypedia before purchase and experimental design.
When searching for a gene or protein in Antibodypedia, a list of all associated gene products is generated displaying gene name and synonyms, description of the gene product, protein family, chromosome location, UniProt id, mouse ortholog, and number of antibodies and providers catalogued in Antibodypedia. From this list, the gene of interest is selected and all available antibodies are presented on the resulting summary page. Filtering options may be used to display only antibodies satisfying desired criteria. The summary page lists the antibodies in an order determined by a scoring and ranking system that is based on the knowledge associated with the antibody; it takes into account the community preference of the antibody in terms of scientific citations and the number of validations performed with the antibody. Information on the type of antibody (monoclonal or polyclonal), number of references, and if the antibody is validated for a certain application is given on the summary page. The validation data is classified into four categories clearly displayed by partially or fully filled green circles. In order to simplify the selection of the most suitable antibody, a function called Compare Selected may be used for detailed studies of the antibodies. The antibodies are lined up side by side with all information to be compared. Once the right antibody has been identified, the direct link to the provider product page may be used.
Due to the complexity in cells and tissues, differences in experimental conditions for various applications, and variation in antibody batches, as much data as possible should be collected on every antibody. Antibodypedia encourages the user community to be active and share their data by uploading conclusive and inconclusive data to the portal. With the gathered knowledge in Antibodypedia you have the power to select the right antibody for the right application.
References and Links
- An article describing Antibodypedia and how to use the database:
Alm, T., von Feilitzen, K., Lundberg, E., Sivertsson, A., & Uhlén, M. (2014). A Chromosome-Centric Analysis of Antibodies Directed toward the Human Proteome Using Antibodypedia. Journal of Proteome Research.
DOI:10.1021/pr4011525. PubMed: 24533432
- The first article about Antibodypedia:
Bjorling, E., & Uhlén, M. (2008). Antibodypedia, a Portal for Sharing Antibody and Antigen Validation Data. Molecular Cellular Proteomics, 7(10), 2028-2037.
DOI:10.1074/mcp.M800264-MCP200. PubMed: 18667413
- Relevant Wikipedia pages:
- Antibodypedia - An open-access database of publicly available antibodies and their usefulness in various applications: