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Protein Forest Inks Two Deals as Effort to Commercialize Technology Intensifies

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This story originally ran on Oct. 20.

By Tony Fong

Technology development and software firm Protein Forest has forged a partnership with Pressure BioSciences and one with a UK proteomics services firm, marking its shift to full commercialization mode.

Last week, the Lexington, Mass.-based firm and PBI, based in South Easton, Mass, announced a collaboration based on each other's technology. And later this week, Protein Forest is expected to ink an agreement with the North East Proteome Analysis Facility in the UK to jumpstart its European operations.

The deals are the first reached by Protein Forest as it seeks to become a viable commercial entity by leveraging its digital ProteomeChip technology, a system that uses parallel isoelectric focusing to fractionate proteins and peptides for mass spectrometry-based analysis and Western blotting.

Both agreements cover co-marketing and sales of the dPC system. In addition, Protein Forest and PBI will co-market PBI's pressure cycling technology for sample preparation. The two firms will also develop new instruments, accessories, and consumables that combine both companies' products.

Meanwhile, NEPAF will also develop workflows and applications for the dPC platform.

From a sales and marketing perspective, the collaboration with PBI is a way of increasing both companies' sales presence without increasing either's marketing budget.

This "pretty much doubles our [sales] outreach right now," PBI CEO Richard Schumacher told ProteoMonitor this week.

The more important long-term benefit, however, is the potential development of new workflows incorporating Protein Forest's technology with PBI's that would significantly reduce the amount of time needed to prepare a protein sample for analysis by mass spectrometry.

While the two companies' platforms are already being used in tandem by some researchers, Protein Forest and PBI will be developing modules to integrate the dPC with the PCT technology, Schumacher said.

After a sample is fractionated by dPC, the proteins need to be digested prior to mass spec. "And there's every indication … that PCT should be able to enhance the workflow of the dPC fractionator," he said.

"We know that there are several labs that are already using [the dPC technology] and our technology separately. But they haven't been integrated," he added. "What we want to see is whether or not you can integrate them to the point where you could almost seamlessly take it from their instrument to our instrument and reduce the amount of work that has to be done in the middle."

The modules that would have to be added to allow that are expected to be "minor," he added.

According to Russell Garlick, president and CEO of Protein Forest, the plan is to speed up both the sample disruption phase of the workflow to minutes from hours, and to develop methods to replace the overnight procedure of in-gel trypsinization to a 15-minute effort with PBI's PCT technology.

If the two firms are successful, it would take researchers one day to "go from a cell to a sample ready for injection onto a mass spec" — a process that can currently take up to three days.

"The laboratory can envision starting at 8 o'clock in the morning, and essentially the sample is ready for mass spec the same day," Garlick said. "Now we can both talk about industrializing proteomics in a one-day procedure."

Both companies declined to disclose the financial terms of the deal.

Planting Roots in Europe

Also, this week Protein Forest expects to formalize an agreement with NEPAF to build workflows and applications based on the dPC platform, expanding its presence in Europe.

A few years back, Northeast England made a push to establish a healthcare and life-science industry in the region, and as part of that initiative, the Boston office of a regional development agency, the North England Inward Investment Agency, had discussions with Protein Forest about opening an office in the Newcastle area.

At the same time, NEPAF had discussions with Protein Forest about creating some kind of working relationship, Glen Kemp, NEPAF's program manager, told ProteoMonitor last week.

In January, Protein Forest announced the opening of its Newcastle-upon-Tyne office with Robert Marchmont in charge. Marchmont has since left Protein Forest, and James Hainsworth has stepped in as the technical support manager at the UK site.

In addition to providing lab space to Protein Forest for use as a demonstration site, NEPAF will provide technical assistance to Protein Forest.

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"One of the issues with the dPC system is that once you've done the analysis, you need to take the chips from the system and do a further analysis to identify which proteins are in which pH fraction of which chip. And that's ideally suited for mass spectrometry," Kemp said. "As a proteomics facility, we have some of the latest cutting edge mass spectrometers. We have an Orbitrap, a Bruker maXis system, so we're well-positioned to do the subsequent analysis for them."

NEPAF is a proteomics services firm that went live a year ago with funding from regional development agency One North East and the European Regional Development Fund [See PM 11/13/2008].

Garlick said the two companies will be working to "establish translational proteomics workflows into protein biomarker-discovery measurement. So on the collaboration side, it's really applying the dPC into quantitative proteomics."

NEPAF has five different mass-spec platforms, and what Protein Forest hopes will result from the collaboration is the development of workflows for each application, Garclick said. "One could be quantitative analysis, one could be global analysis, and one could be glycoprotein analysis," he said. "We're looking for them to identify the most appropriate mass-spec platform for those particular platforms."

Protein Forest has a similar collaboration with Thermo Fisher Scientific's Biomarker Research Initiatives in Mass Spectrometry Center, and the work at NEPAF will augment that research. Protein Forest is not a mass-spec company, "so it behooves us to work with teams that are very, very smart and expert in mass-spec detection methods so they can make recommendations to the ultimate end-user who's a biologist or molecular biologist on how to do the detection," Garlick said.

Protein Forest and NEPAF will also co-market each other's products and services. Kemp said that NEPAF is not explicitly endorsing Protein Forest products, but "we certainly do see opportunities where [dPC] has specific applications, and in those cases, we'll be quite happy to highlight to our customers that this is a machine that can do a specific task that will answer some of their problems."

From Do-Over to Creating Market Presence

The two deals represent the next phase in Protein Forest's progression from a start-up technology development firm that was forced back to square one when its original design for the dPC technology couldn't fly, to a company now trying to reap the rewards from the technology.

The company was founded in 2002 by the three Israeli physicists who developed the ProteomeChip technology — Shmuel Bukshpan, Uri Halavee, and Gleb Zilberstein — and PureTech Ventures [See PM 11/28/03].

But one year after the company began developing the technology for commercial use, it realized the chips could not identify proteins. Protein Forest was forced to start over from scratch [See PM 05/10/07].

Last year, five years after it first set out developing the dPC technology for commercial use, the company launched the dPC system at the annual conference of the American Society for Mass Spectrometry. In March, Protein Forest hired John Tonkinson in the newly created position of vice president of global sales and marketing, to support commercialization of dPC.

According to Protein Forest's website, ProteomeChip works in the following manner: proteins and peptides are charged "in an environment that is either above or below their isoelectric points, allowing them to migrate in an electric field." The charged peptides/proteins travel through the dPC chip between the acidic and basic sides of the chip. Once they hit a gel plug near their isoelectric point, they become neutral. "The uncharged protein or peptide will no longer migrate and will become enriched and separated from other proteins with slightly different isoelectric points," the company said.

Because the separation is done in a "unique parallel format … we're doing very fast isoelectric trapping" with very high field strengths, Garlick added. Unlike IPG strips, which are based on linear gradients, the dPC technology has discrete pH units, which result in "much faster isoelectric separation."

The dPC platform is meant to replace longstanding approaches such as IPG strips and 2D gel strategies, as well the strong cation exchange chromatography, Garlick added.

In addition to faster separation speeds, reproducibility is improved "because we can accurately and precisely measure the pH of each of our gel features," he said. While he declined to provide specific sales numbers, he said that market reception to the system has been "very good. We get a lot of 'Wow, you can do that in 30 minutes?'"

The instrument, priced at $20,000, simultaneously runs six strips, which are available for protein separation and for peptide separation.

The instrument is initially targeted for core facilities and the molecular biologists who use such facilities, Garlick said. The company, he added, is on the prowl for other deals as well, similar to the PBI and NEPAF partnerships.

In the end, to make the proteomics workflow effective, "customers don't want to have to do all the shopping themselves," he said. "Vendors that put the workflows together with defined protocols are providing a terrific service to the customers, so that's what we're doing."

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