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HUPO 2013 Sees New Instrument Launches, Efforts to Envision Proteomics Tools of the Future

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Proteomics instrumentation, both newly launched and merely proposed, grabbed a share of the spotlight at the Human Proteome Organization's 12th annual meeting this week in Yokohama, Japan.

In addition to updates from the organization's many initiatives, the conference saw new mass spec releases from vendors including Bruker and Thermo Fisher Scientific, as well as the beginning of formalized efforts to envision what the proteomics instrumentation of the future might look like.

Thermo Fisher, for instance, launched its new Q Exactive Plus, an updated version of its popular Q Exactive instrument, that features enhancements throughout its ion transmission system, allowing for better sensitivity and improved performance in data independent acquisition workflows (PM 9/13/2013).

The company also launched its new Exactive Plus EMR (extended mass range) instrument, which is targeted at the analysis of intact proteins and protein complexes, a field that has traditionally been dominated by QTOF systems.

Bruker, meanwhile, launched its own instrument aimed at the intact protein space, its Maxis HD QTOF, a system, the company said, intended for top-down proteomics and biopharmaceutical characterization. According to Bruker, the Maxis features full sensitivity resolution greater than 75,000 and a dynamic range of five orders of magnitude.

Beyond the new releases, the meeting also offered a glimpse of the field's vision for future instrumentation with a session led by Bruno Domon, head of the Luxembourg Clinical Proteomics Center, focused on sketching out designs for analytical platforms capable of routine proteomic experiments.

While proteomics has over the last decade begun to see uptake by non-specialists, the discipline – especially with regard to mass spec-based work – still remains largely the province of experts and core laboratories. This is due in no small part to the complexity and expense of the mass spec instrumentation used by the field – a fact that has led to interest among researchers and vendors in developing simpler, cheaper systems that could be employed, for instance, by non-expert biologists in their labs.

Swiss Federal Institute of Technology Zurich researcher Ruedi Aebersold, for instance, has told ProteoMonitor, that he envisions a future in which "a biologist in a laboratory who is doing quantification of proteins by Western blotting would have access to a mass spectrometer and they could say, 'I need to measure these 60 proteins over 100 strains,' and they could simply download the assays and do the measurements" (PM 1/25/2013).

With this aim in mind, Aebersold and his colleagues have been generating reference spectra libraries for various proteomes of interest, which will allow researchers to measure these proteins via either shotgun or targeted mass spec without the need for extensive assay development. However, the complexity of current mass spec instrumentation remains a limiting factor.

This week's HUPO session, in which Aebersold participated as chair of a working group, aimed to outline requirements for two models of what the organizers termed a "proteome analyzer." The first, a high-throughput Western blot-like analyzer, would allow biologists to perform targeted identification and quantification of proteins in a sample. The second would be an instrument that would enable proteomic projects analogous to RNA-Seq experiments, allowing researchers to perform quick, systemic analyses of large numbers of proteins.

In addition to Aebersold, the session's working groups were chaired by Mark Cafazzo, global market manager, proteomics at AB Sciex; Stanford University researcher Michael Snyder; and Andreas Huhmer, proteomics marketing director at Thermo Fisher.

Vendor participation will obviously be key to any such instrument development efforts, and, in past interviews with ProteoMonitor, representatives from firms including Thermo Fisher, AB Sciex, and Agilent have expressed interest in the notion of building simpler, less expensive instruments for proteomic analyses. Appropriately balancing questions of cost versus performance versus ease of use remains a considerable challenge, however, as does demonstrating sufficient researcher demand to justify the investment required to build and market such an instrument.

As Ian Jardine, Thermo Fisher's vice president of global R&D, told ProteoMonitor in an interview earlier this year, such an instrument does have precedent in the marketplace. Thermo Finnigan in 2002 launched its ProteomeX instrument, an integrated LC-MS/MS system designed for easy mass spec analysis of proteins.

"We actually sold many hundreds of that system," Jardine said. "It did quite well, but it kind of got supplanted when we put out the LTQ-FT and then the LTQ-Orbitrap. The automated, integrated system kind of fell by the wayside at that point."

Beyond mass spec-based tools, this week's meeting also saw updates on a number of other resources central to the field. Notably, Royal Institute of Technology Sweden researcher Mathias Uhlen presented on the current edition of the Human Protein Atlas, which seeks to validate antibodies to the entire human proteome.

According to Uhlen, the HPA currently contains information on more than 18,000 validated antibodies to 15,000 gene products, which corresponds to 75 percent of the protein-encoding genes in humans. Combining this antibody data with transcriptomic data, the effort has developed a map of proteins across all major human organs and tissues.

Several proteomics informatics resources also provided updates. Researchers from the Swiss Institute of Bioinformatics' neXtProt platform announced that the resource has developed a pipeline for integrating all human peptide identifications from the PeptideAtlas repository and has, to date, integrated 279,933 identified peptides mapped to 14,131 proteins along with 32,521 post-translational modifications.

Researchers from the ProteomeXchange consortium, which aims to coordinate the global deposition and sharing of mass spec-based proteomics data, announced that as of July 2013 the resource has received 310 submissions of mass spec data from 28 countries totaling roughly 20 terabytes.

And researchers from the Beijing Proteome Research Center announced the development of a new proteomics resource, the Human Proteome Knowledge Discovery Gateway, which aims to integrate heterogeneous proteomic datasets along with tools for applications including integrating proteomic and genomic data; gene ontology enrichment searches; and network and pathway analyses.