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EU Funds $11.5M Initiative to Offer Proteomics Services and Drive Tool Development

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By Adam Bonislawski

The European Union's Seventh Framework program will provide €8 million ($11.5 million) over the next four years for proteomics research to be performed by the PRIME-XS consortium, a group of proteomics research teams from 12 European institutes.

The initiative will support technology and method development work by the 12 teams as well as provide funds for proteomics services for an anticipated 150 to 200 research projects chosen via a competitive review process.

According to Reinout Raijmakers, managing director of the Bijvoet Center for Biomolecular Research at Utrecht University and part of the PRIME-XS management-support team, the project is the first of its size focused on proteomics launched by the EU and demonstrates the body's growing interest and confidence in the field.

"[Funding] within the Seventh Framework is always dependent on what the EU considers important at that time, and the EU has seen over the last few years [that] proteomics has really been booming," Raijmakers told ProteoMonitor. "It's a very fast moving field where a lot of development has gone on over the last few years, and [it] now has reached a level where it can be applied to many research subjects and be of value to many scientists in the life sciences."

While there have been other proteomics initiatives at the national level in Europe, such as the German Brain Proteome Project, and the UK's Structural Proteomics of Rational Targets initiative, "the EU saw that now the time was right to set up [such an initiative] at the European level," Raijmakers said.

Formation of the PRIME-XS consortium began in 2009 with a call from the EU for an initiative focused on proteomics, he said. Over the next two years, under the coordination of Netherlands Proteomics Centre scientific director Albert Heck, the 12 participating institutes were recruited.

This week PRIME-XS officially began accepting research proposals from scientists requesting access to one of the six facilities providing proteomics work.

These access facilities are the Netherland Proteomics Centre in Utrecht; the VIB Proteomics Unit in Ghent; the University of Zurich's and ETH Zurich's Functional Genomics Center; the CRG/UPF Proteomics Unit in Barcelona; the UK's Cambridge Center for Proteomics; and the CEA Proteomics Technological Platform in Grenoble. Between them they will offer more than 50 different mass spectrometers and associated proteomics tools for use on the accepted proposals.

Additionally, scientists from the University of Copenhagen; Vienna's Research Institute of Molecular Pathology; the Eberhard Karls University, Tübingen; the European Bioinformatics Institute; and the Max Planck Institute of Biochemistry will develop tools and methods for the initiative.

The effort includes a number of industry partners, as well, with vendors such as AB Sciex, Agilent, Bruker, Thermo Fisher Scientific, and Waters providing "advice, instructions, and perhaps demo software or discounts for users," Raijmakers said.

The R&D portion of the initiative, Raijmakers noted, will focus on devising techniques to continue moving proteomics beyond simply identifying and quantifying proteins present in samples to monitoring the changing states and localization of proteins in vivo.

"What we can do right now is basically look at all the proteins that are in an organism or cell," he said. "But many of these proteins are modified over time and [undergo] continuous changes. In addition, a protein isn't always in the same location in a cell but can move through a cell, and this can have an impact on the other proteins in those locations.

"So one of the things we're trying to do among others is develop methods to look at these particular aspects of proteins," Raijmakers added. "How do they change chemically over time? What other proteins do they interact with? Where in the cell do they do this?"

The proteomics services portion of the initiative, by contrast, has no particular focus but is open to any scientist – academic or industry – from one of the 40 EU or EU-associated countries affiliated with the Seventh Framework Program.

"Interested scientists have to write a proposal in which they explain why they feel this research needs to be done and why proteomics is important to achieving the research," Raijmakers said. "Then the reviewers look at the proposals and aspects like whether proteomics is really essential [to the work] and [whether] it is a significant contribution to science."

He estimated that the consortium would be able to perform between 150 and 200 research projects over the four-year period, with a total execution time of around 2,000 days.

Beyond providing services to researchers, the initiative also aims to offer training in proteomics – a growing need, Raijmakers suggested, given the discipline's growth beyond the confines of mass-spec experts.

"It's not like people will be given time on a [mass-spec] instrument and we just wish them good luck with it," he said. "If they have a project approved they come into contact with a proteomics expert at a particular access site who will discuss how the experiment needs to be done to make sure we get results the biologist will find useful, and they will get assistance in executing the steps needed to come to these results."

"We're trying to provide full support for people who don't have expertise in mass spectrometry to do these types of experiments," Raijmakers added. "They'll get basic training in sample preparation, data analysis, interpretation. They'll be trained at a basic level in proteomics – the level they need to work on their own projects."

The initiative is also offering formal courses for researchers covering both basic and advanced proteomics topics and techniques, he said.

Research proposals will be approved on a rolling basis throughout the four years of the project with no deadlines for submission, Raijmakers said. He noted, however, that if interest turns out to be very high PRIME-XS could move to a "step-based admissions system where every few months we judge all the proposals" submitted within a given timeframe.

He added that, if successful, the program could be extended past its current timeline, although this would require that the consortium apply for an extension of its funding at the end of the four years.


Have topics you'd like to see covered in ProteoMonitor? Contact the editor at abonislawski [at] genomeweb [.] com