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IP in Hand, Proteomics Start-Up Proteomyx Says Its Technology Can Replace Mass Spec

Proteomyx, which has developed technology that its founder says allows researchers to analyze proteins differentially without the use of mass spectrometers, recently received its second US patent, in what its owner hopes will be a steppingstone toward financial sustenance.
The patent, No. 7,175,986, was awarded on Feb. 13, and according to its abstract, the technology “has many applications in comparing and panning for differentially abundant molecules or differential modification of molecules for proteomics, glycomics, phospho-proteomics, metabolomics, [and] epigenomics.”
“The patent is important because people can use existing technology to perform this entire process,” Proteomyx’s founder and owner, Nathaniel Tran, told ProteoMonitor last week “The patent is what we need to get ourselves out there and give ourselves credibility.”
The company’s first patent, No. 7,029,855, was awarded last April. According to its abstract, “The novel technique exploits the differences in radiation energy or half-life between isotopes to make differential detection and quantification of labels possible.”
Like most other start-ups, Proteomyx, founded in 2003, has survived on bread and water. To date, Tran has spent about four years funding the company out of his own pocket, working three other jobs. And if it takes a few more years to get the company to financial self-sufficiency, he said, he’s ready to keep at it.
“I can go pretty long, yeah, a few more years easily,” said Tran, who emigrated to this country from Vietnam when he was 16.
Replacement for MS?
The technology Tran developed, called Differential Proteomic Panning, involves methods and reagents for labeling molecules in multiple samples, then combining and selecting labeled molecules from unlabeled ones for use in simultaneous co-assaying analysis.
Two samples are tagged with different radioactive reagents — Tran has been using tritium and carbon 14 —and mixed together. The compounds are then separated by chromatography. Each separate fraction is checked for the expected ratio of radioactive reagents. Those with an abnormal ratio are examined for responsible molecules while those with normal ratios are run through the chromatographer using a different means of separation.
“My [technology] basically uses radiochromatography [to] compare the isotope ratio, and when you have a deviation in isotope ratio, you know there’s a differential abundance,” he said. “You select that fraction and zoom it in and go after the protein of interest.”
According to Tran, DPP offers several advantages to other labeling techniques: Because it does not require proteins to be chopped into peptides for analysis, whole proteins can be analyzed and their behaviors in protein-protein interactions can be studied. Tran also says that low-abundance proteins are less likely to be missed due to masking by high-abundance proteins.
“It reduces the amount of work tremendously. It allows you to discard a lot of things along the way, irrelevant fragments along the way,” Tran said. The amount of time needed to sift through the gargantuan amount of mass spectra data will be reduced from months to a day, Tran claims.
And because a mass spectrometer is not needed, the analysis is cheaper to carry out.
“Most people do not have the resources to buy an expensive mass spectrometer in order to access the latest technology. We’re talking $300,000 [for the instrument] plus $100,000 a year to run it,” Tran said. “At the end, they still use a little bit of mass spec, but they can send that to a contact lab.”
By comparison, it will cost about $500,000 to license DPP, depending on the size of the company and its R&D budget, said Tran.

“Most people do not have the resources to buy an expensive mass spectrometer in order to access the latest technology. We’re talking $300,000 [for the instrument] plus $100,000 a year to run it. My technology would give those people the chance to do cutting-edge proteomics.”

Proteomics Entrepreneur

Prior to forming Proteomyx in 2003, Tran, 33, worked as a scientist at drug maker Allergan. It was there that he became interested in proteomics and tried to get his employers to incorporate proteomics methods — mostly 2D gel work — into its research methods, he said.
At the same time, he also saw that there were gaps in proteomics technology, particularly labeling techniques, which needed to be addressed if proteomics was to move forward as a research discipline. So he founded Proteomyx and incorporated it as an S corporation. When he quit his job at Allergan in 2004, he began developing Proteomyx and the DPP technology in earnest.
Since forming the company, Tran has split most of his time between getting the DPP technology patented and trying to drum up interest in it. Companies he initially contacted included Beckman Coulter and Amgen. Each told him the technology was not ready for commercialization.  
“They want to wait to see more results,” he said. One drug company, which he declined to identify, told him that it wanted to see that DPP would be applicable to their drug-discovery work and platform.
“What I have is a run of a few proteins,” Tran said.
He is now hoping that with two patents in hand, the company can gather some momentum. At the Pittsburgh Conference in Chicago last week, Tran manned a booth he shared with another start-up, Cal-Tech Scientific — for whom he does some marketing and business development in return for access to their facility and instruments — while chatting up other companies to gauge their interest in licensing the technology and perhaps entering into distribution deals with Proteomyx.
Among the companies he spoke with were Merck, Amgen, Pfizer, PerkinElmer, Bio-Rad Laboratories, and American Radiochemical. At this point, discussions are preliminary, though Tran said a few companies have expressed interest in the DPP platform.
Because Proteomyx has yet to generate any revenues, Tran has subsidized the company through a job buying and selling lab equipment and also exporting wine to Vietnam, he said. To date, he added, he has spent about $150,000 to $200,000 on Proteomyx.
In a year from now, he said, he would like to have one company licensing the DPP technology. In addition, he expects to have one study out verifying the utility of the technology.

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