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Researchers Showcase Results, Look to Future Efforts as EU Prime-XS Proteomics Initiative Winds Down

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NEW YORK (GenomeWeb) – With the EU-funded Prime-XS proteomics initiative winding down, participants showcased the fruits of their labors with a special issue last month in Molecular & Cellular Proteomics focused on work that has emerged from the project.

Featuring 19 papers detailing proteomics research done through the initiative, the issue will hopefully demonstrate to EU officials the value of the project and the value of further investment in proteomics more generally, Ruedi Aebersold, a researcher at the Swiss Federal Institute of Technology Zurich and a project participant, told ProteoMonitor.

Launched in 2011 with €7.8 million ($10.1 million) in funding under the EU's Seventh Framework Programme, Prime-XS was intended to both further proteomics technology development and to broaden researcher use of proteomics technology by funding free access to state-of-the-art proteomics research facilities.

"The idea was that proteomics has made a lot of progress over the last decade or so, but compared to genomics the uptake and dissemination of proteomics to mainstream biology has been much slower," Aebersold said. "And so the pitch was that there would be resources generated and access centers created so that scientists like biologists and clinicians who do not have access to high-end proteomic methods would get access through Prime-XS."

The project gathered together 12 leading proteomics research centers across Europe, including six – the Netherlands Proteomics Center, the VIB Proteomics Unit, the Functional Genomics Center Zurich, the CRG Proteomics Unit, the Cambridge Centre for Proteomics, and the CEA Proteomics Unit – to which outside scientists could apply for free access to proteomic technology for performing their research. In total, the initiative funded 1,971 days of researcher access to the proteomics centers.

Establishing specific criteria to measure the success of the project was somewhat difficult, Aebersold noted. "Do you say [for instance], that it is a success if 100 people use a [proteomics] lab."

One relatively straightforward measure, though, is the number of published papers to come out of the project. And, Aebersold suggested, by this measure, Prime-XS has been a success, with some 90 papers coming out of work done through the initiative.

In addition to providing access to existing proteomics technology, the project also aimed to develop and disseminate new proteomics technologies. For instance, Aebersold noted, the lab of Albert Heck, chair of the Biomolecular Mass Spectrometry and Proteomics group at Utrecht University and head of the Prime-XS project, developed methods for improving the robustness of phosphopeptide measurements that were used in a number of studies conducted as part of the initiative.

Aebersold's group, meanwhile, focused on developing targeted biomarker assays, providing researchers with validated multiple-reaction monitoring mass spec assays for a number of glycoproteins.

"We have been working on these targeted methods for quite a while," Aebersold said. "And in the context of Prime-XS it was our task to develop validated targeted assays for certain proteins and make them accessible."

The Prime-XS initiative is scheduled to end in January 2015, and while the number of publications linked to the project would suggest that it has been a success, it remains to be seen whether researchers who took advantage of the free access to proteomics facilities it offered will continue to use proteomics in their work now that they will have to pay for such analysis themselves.

"This is an important question," Aebersold said. "One mechanism of providing access [will have] disappeared, but I think it's fair to say that those in the research projects benefited and they forged connections and now know how to use these [proteomic techniques]. So they now can probably go to other core labs or access centers and do their experiments, because once you know how this works, the threshold is much lower."

Also an important consideration for EU-based proteomics researchers is the extent to which the results of Prime-XS can be leveraged into additional funding for future proteomics initiatives.

The MCP special issue, Aebersold said, is intended in part to help with this process by providing a solid example of the project's value.

"Proteomics is still under-disseminated, and I think this special issue makes a collection of papers to demonstrate to the [EU] politicians and program managers that something tangible came out [of the project]," he said.

He cited the example of the EU-funded Proteomics Specification in Time and Space (Prospects) project, which likewise published a special issue in MCP that, he said, "was extremely well received" by Seventh Framework Programme managers.

EU science funding is now operating under the Horizon 2020 framework program. Aebersold said that there are currently no firm plans in place for another project similar to Prime-XS but that he expects proteomics researchers to apply when calls for projects are announced.

He suggested two areas in which such a future project might focus – use of protein cross-linking combined with mass spec for structural analyses, and the development and dissemination of data independent acquisition mass spec approaches like the Swath technique developed in his lab.

"I think these are both fairly robust now and they interface very nicely with what biologists [outside proteomics] are doing," he said.

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