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Antibodypedia: a portal for sharing antibody and antigen validation data
KTH, School of Biotechnology (BIO), Proteomics.
KTH, School of Biotechnology (BIO), Proteomics.ORCID iD: 0000-0001-8993-048X
2008 (English)In: Molecular & Cellular Proteomics, ISSN 1535-9476, Vol. 7, no 10, 2028-2037 p.Article in journal (Refereed) Published
Abstract [en]

Antibodies are useful tools to characterize the components of the human proteome and to validate potential protein biomarkers discovered through various clinical proteomics efforts. The lack of validation results across various applications for most antibodies often makes it necessary to perform cumbersome investigations to ensure specificity of a particular antibody in a certain application. A need therefore exists for a standardized system for sharing validation data about publicly available antibodies and to allow antibody providers as well as users to contribute and edit experimental evidence data, including data also on the antigen. Here we describe a new publicly available portal called Antibodypedia, which has been developed to allow sharing of information regarding validation of antibodies in which providers can submit their own validation results and reliability scores. We report standardized validation criteria and submission rules for applications such as Western blots, protein arrays, immunohistochemistry, and immunofluorescence. The contributor is expected to provide experimental evidence and a validation score for each antibody, and the users can subsequently provide feedback and comments on the use of the antibody. The database thus provides a virtual resource of publicly available antibodies toward human proteins with accompanying experimental evidence supporting an individual validation score for each antibody in an application-specific manner.

Place, publisher, year, edition, pages
2008. Vol. 7, no 10, 2028-2037 p.
Keyword [en]
B-CELL EPITOPES; HUMAN PROTEOME; CANCER TISSUES; RESOURCE; ATLAS; GENERATION; PREDICTION; PEPTIDES; PROTEINS; ENSEMBL
National Category
Industrial Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-9746DOI: 10.1074/mcp.M800264-MCP200ISI: 000260424700019Scopus ID: 2-s2.0-53249092612OAI: oai:DiVA.org:kth-9746DiVA: diva2:127401
Note
QC 20100708Available from: 2008-12-05 Created: 2008-12-05 Last updated: 2011-09-05Bibliographically approved
In thesis
1. Databases for antibody-based proteomics
Open this publication in new window or tab >>Databases for antibody-based proteomics
2008 (English)Doctoral thesis, comprehensive summary (Other scientific)
Abstract [en]

Humans are believed to have ~20,500 protein-coding genes andmuch effort has over the last years been put into the characterizationand localization of the encoded proteins in order to understand theirfunctions. One such effort is the Human Proteome Resource (HPR)project, started in Sweden 2003 with the aim to generate specificantibodies to each human protein and to use those antibodies toanalyze the human proteome by screening human tissues and cells.The work reported in this thesis deals with structuring of data fromantibody-based proteomics assays, with focus on the importance ofaggregating and presenting data in a way that is easy to apprehend.The goals were to model and build databases for collecting, searchingand analyzing data coming out of the large-scale HPR project and tomake all collected data publicly available. A public website, theHuman Protein Atlas, was developed giving all end-users in thescientific community access to the HPR database with proteinexpression data. In 2008, the Human Protein Atlas was released in its4th version containing more than 6000 antibodies, covering more than25% of the human proteins. All the collected protein expression datais searchable on the public website. End-users can query for proteinsthat show high expression in one tissue and no expression in anotherand possibly find tissue specific biomarkers. Queries can also beconstructed to find proteins with different expression levels in normalvs. cancer tissues. The proteins found by such a query could identifypotential biomarkers for cancer that could be used as diagnosticmarkers and maybe even be involved in cancer therapy in the future.Validation of antibodies is important in order to get reliable resultsfrom different assays. It has been noted that some antibodies arereliable in certain assays but not in others and therefore anotherpublicly available database, the Antibodypedia, has been createdwhere any antibody producer can submit their binders together withthe validation data in order for end users to purchase the bestantibody for their protein target and their intended assay.

Place, publisher, year, edition, pages
Stockholm: KTH, 2008. 68 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2008:24
Keyword
proteomics, antibodies, database, biomarker, website
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-9658 (URN)978-91-7415-161-9 (ISBN)
Public defence
2008-12-19, FD5, AlbaNova, Roslagstullsbacken 21, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
QC 20100708Available from: 2008-12-05 Created: 2008-11-24 Last updated: 2010-07-08Bibliographically approved

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