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Protein Forest Preps To Bring Chip to Market in 2008


Building on technology that failed the first time around, Protein Forest is ramping up to launch its first commercial product, a chip allowing researchers to separate proteins based on their isoelectric point.

Headquartered in Waltham, Mass., Protein Forest was launched in 2002 and, like many startup technology companies, found flaws in its original product design. So it went back to the drawing board, did further development, and after five years, the company is now beta testing the chip in anticipation of its launch onto the commercial market early next year.
Protein Forest received US patent number 7,166,202 titled “Matrixes, arrays, systems and methods” for the chip in January and has two other patents pending.

The chip is based on the company’s digital ProteomeChip technology, which relies on well-established isoelectric principles. The advantage of the dPC technology, the company says, is significantly quicker separation time and ease of use.

Protein Forest began developing the chip in 2003 after receiving its first round of venture capital funding of $12 million. But after a year in development, it became clear that there would not be a market for it. The problem was that proteins could not be identified with the chip, says Russell Garlick, currently the chief technology officer of the company and Protein Forest’s original president and CEO.

“Those were just spots on an image; you really couldn’t identify them,” he says. “We never really did quantitative analysis or characterization [of the proteins], so we never knew how many proteins there were.”

Because of its size, 1 centimeter by 1 centimeter, the chip was too small to produce enough proteins for protein identification, and so couldn’t be used for mass spectrometry sample preparation, he says.

“It just never proved to be a product that could meet the manufacturing cost and reproducibility [criteria] that the company set,” Garlick says.
 —Tony Fong

Short Reads

Proteome Systems licensed its Eukarion portfolio to Minerva Healthcare for $4 million, as well as a 10 percent stake in Minerva and payments for clinical development and product sale royalties. This portfolio contains small-molecule drug compounds, and Minerva is developing therapeutics for dermatological diseases.

Expression Pathology and Oridis Biomed will be offering proteomic tissue-analysis services for protein biomarker research to drug-development, medical-diagnostic, and academic customers.

Northeastern University and Waters opened a new mass-spectrometry lab with four of the company’s mass spectrometers. The Waters Mass Spectrometry Laboratory will be researching the shape and characteristics of proteins for treatment development.

National Institutes of Health awarded Protein Discovery a $750,000 phase II Small Business Innovation Research grant. The company will develop its MALDIplex M5 sample-prep platform used in protein and small-molecule mass spectrometry-analysis studies.

The University of Copenhagen received a grant worth $109.1 million from the Novo Nordisk Foundation. The university plans to open the Novo Nordisk Foundation Center for Protein Research next year for research on the role and function of proteins in both healthy and sick people.


US Patent 7,211,791. Method and apparatus for chromatography-high field asymmetric waveform ion mobility spectrometry. Inventor: Raanan Miller, Erkinjon Nazarov, Gary Eiceman, Evgeny Krylov, and Boris Tadjikov. Assignee: Charles Stark Draper Laboratory. Issued: May 1, 2007.

This patent describes a “method and apparatus for chromatographic high field asymmetric waveform ion mobility spectrometry.” To partially separate sample compounds before ionization, the apparatus includes “a gas chromatographic analyzer section intimately coupled with an ionization section, an ion filter section, and an ion detection section.”

US Patent 7,208,729. Monolithic micro-engineered mass spectrometer. Inventor: Richard Syms. Assignee: Microsaic Systems. Issued: April 24, 2007.

This patent covers “a method of constructing a micro-engineered mass spectrometer from bonded silicon-on-insulator wafers” whose “quadrupole geometry is achieved using two BSOI wafers, which are bonded together to form a monolithic block,” and whose “deep etched features formed in the inner silicon layers are used to define ion entrance and ion collection optics.”

Data Point

$1.2 million

The National Institutes of Health awarded Phoenix S&T $1.2 million in a phase II SBIR grant. Phoenix S&T will be developing a prototype microfluidic chromatographic device that uses nanoparticles to separate glycoproteins that may be used as biomarkers for disease.