Outcomes of the ProteomeBinders Project

In the four project years (March 2006 – May 2010) ProteomeBinders has gained international recognition as a major ‘think tank’ in the field of affinity reagents for proteomics. The consortium has gained wide recognition through publications, media articles, press releases, meetings organised, workshop and conference participation and this website.

Particular archievements are:

  1. The web portal Antibodypedia (www.antibodypedia.org) is a database through which users can obtain application-specific validation data for publicly available antibodies. The Antibodypedia has been developed at partner KTH within the ProteomeBinders consortium and has been a publicly available resource since September 2008. The binders have been validated by users in 21269 experiments (as of September 2010). Its main features are:
    – annotation of antibodies and target proteins
    – detailed results of key quality control assays (array, immunohistochemistry, immunofluorescence, western blot) with results available online
    – validation scoring system, colour coded to indicate suitability of binders for different applications, at a glance
    – external submissions to the database are welcomed
    – current content of 7105 reviewed binders, covering 5688 genes
  2. EMBL Heidelberg has completed the development of a set of networking tools known as EPIC, the Epitope Choice Resource, for the construction of a proteome scale epitope selection pipeline. EPIC interacts with a wide range of bioinformatics software and biological data annotation to achieve a unified view of a target protein and allow the user to identify suitable regions of the protein to raise antibodies against. It is a freely available web resource for the proteomics community
  3. ENSEIRB and EMBL/EBI have developed a binder ontology and data exchange format (PSI-PAR) and introduced the Minimum Information about a Protein Affinity Reagent (MIAPAR), defined guidelines for reporting of affinity reagents. The PSI-PAR format is a standardised representation of protein affinity reagent data and is designed to facilitate the exchange of information between different databases and LIMS systems. The MIAPAR standard is a set of guidelines for experimentalists to unambiguously describe protein affinity reagents and their protein targets. It specifies the minimum amount of information which should be present in any publication, database entry or commercial catalogue describing either the production or use of affinity reagents. It has been published in Nature Biotechnology and is regarded as an important contribution to binder description standards.
  4. ProteomeBinders has also been a leading partner in an international SH2 binder pilot project for generation of renewable affinity reagents [ref] , which provided an opportunity to put the designs into practice. In this multicentre pilot study, the aim was to assess the potential of hybridoma and recombinant display technology in large-scale antibody generation. Twenty different SH2 domain proteins were produced as targets (by the Structural Genomics Consortium) and binders generated in five different laboratories. The project generated a set of useful reagents that will be made available to the research community without restriction on use and clearly demonstrated the potential for antibody generation within a larger scale project. It also led to some important pointers for productivity in a larger project. Thus, while binders could be produced in large numbers and their specificity ascertained, downstream biological validation and quality control is the most work-intensive step in this process and will benefit most from optimisation and streamlining.
  5. Links have been made to a parallel initiative of the National Cancer Institute in the USA, which is creating an affinity binding molecule resource against cancer targets in its clinical proteomics programme, and to the antibody and proteome standards initiatives of the human proteome organisation (HUPO). Recently, several ProteomeBinders partners have been invited to the NIH to participate in a workshop on the US programme in October 2010
  6. To complement the networking activities within the ProteomeBinders CA with practical laboratory work towards the establishment of a binder infrastructure, partners from the ProteomeBinders consortium are engaged in two FP7 projects, entitled AffinityProteome and AFFINOMICS. AffinityProteome, under the call for “Research for the benefit of SMEs” from the DG Health, started in March 2009, linking 11 partners (5 of them SMEs) in order to raise binders against signal transduction molecules of the MAPK and TGF-beta pathways. AFFINOMICS links 15 partners, of whom 12 were also partners in ProteomeBinders, and will run for 5 years from April 2010, with an EC contribution to funding of 11M€. The aim is to produce a repertoire of binders against 1000 proteins involved in signal transduction and cancer and as biomarkers.
  7. The consortium has published major papers on the prospects for a European binder resource, the web facilities of Antibodypedia and EPIC, PSI-PAR, and the MIAPAR standard, outputs of the SH2 pilot, etc. Journals have included Nature Methods, Nature Biotechnology, Trends in Biotechnology, Proteomics and Molecular and Cellular Proteomics.
  8. The Project has organised two major open workshops on Affinity Proteomics, at the Alpbach conference centre, the most recent in March 2009, in collaboration with the European Science Foundation, which have been attended by over 100 participants each. A number of other important workshops and conference symposia have also been organised within the scope of the programme.