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FEATURE: How to Build a Proteomics Company

NEW YORK, June 8 – What would you do if you had all the money in the world to build a proteomics company?


Stephen Naylor, the director of biomedical mass spectrometry and functional proteomics at the Mayo Clinic, in Rochester, Minn., has his plan figured out. In a conference call Friday morning, coordinated by Jim Reddoch of Banc of America Securities, Naylor laid out the nuts and bolts of his hypothetical company, for the benefit of investors in proteomics technology.


But just because Naylor was given a blank check doesn’t mean he thinks his company should tackle full-fledged proteomics, which he described as identifying and characterizing every protein in the human body.


“I wouldn’t form a straightforward proteomics company where I would be looking to determine the complete proteome of a human being,” he said. “That space is going to be occupied by the 800 pound gorillas such as Celera, OGS, and GeneProt.”


Nor would Naylor steer his company toward structural proteomics, because solving protein structures using NMR or x-ray crystallography is difficult, and therefore “relatively slow.”


Instead, Naylor said his imaginary company, which he declined to name, would dive into differential and functional proteomics, that is, quantifying differences in proteins between healthy and diseased cells and studying their roles in the body. Such a company would have the goal of developing new diagnostics, panel screens, and therapeutics, he said.


The first step in building such a company would be to form strategic partnerships with medical institutions to get a hold of tissue or cell samples, Naylor said. To process these samples, he advocated a two-pronged approach, combining 2-D gel electrophoresis technology with liquid chromatography, before ciphoning the samples toward mass spectrometry for analysis.


Of the 2-D gel technology platforms, Naylor said he preferred Amersham Pharmacia Biotech’s differential fluorescence platform, because of its “powerful presence in the 2-D world.” The technology is superior, he said, because the platform allows scientists to analyze healthy and disease samples simultaneously, rather than analyze two separate gels to make a comparison.


But Naylor said he would place a heavier emphasis on liquid chromatography as a separation technique, because it can separate proteins in a matter of hours, rather than the days it takes to separate proteins using 2-D gels. Naylor’s favorite supplier of liquid chromatography, or LC, equipment is Michrom, based in Auburn, Calif., because it has developed small capillary columns most compatible with his mass spectrometry technology of choice.


Mass spectrometry, Naylor said, does the real donkey work when it comes to proteomics. To start off, Naylor would purchase a series of quadrupole time of flight, or QTOF, and electrospray LCT mass spectrometers from Micromass, based in Manchester, UK. In addition, he would also purchase ion trap mass spectrometers from Bruker Daltonics. “This decision is based on what’s happening today,” cautioned Naylor.


Other companies, such as PE Sciex, Applied Biosystems, Thermo Finnigan, are all developing potentially more powerful technologies, but currently Micromass instruments have the most valuable software capabilities. 

In addition to mass spectrometry instruments, Naylor also added surface plasmon resonance technology to his wish list.


Surface plasmon resonance, or SPR, uses variations in reflected laser light to probe protein-protein, or protein-

drug interactions. Biacore, based in Uppsala, Sweden, is currently the leader in SPR technology, he said, but HTS Biosystems, of Hopkinton, Mass., has also developed a flexible approach to studying interactions that can be easily coupled with a mass spectrometer.


Lastly, to make all the data comprehensible, Naylor said his company would require a significant investment in bioinformatics. “The company has very sophisticated technology, and we’d be able to produce up to a terabyte of data,” he said. “We would need data analysis, storage, data mining, and the ability to make predictions using computational biology.”


Naylor mentioned GeneLogic, Compugen, and Incyte as initial players in the field, with IBM, Oracle, and Compaq also developing bioinformatics services and products. But the most promising two conglomerates, he said, looked to be Applied Biosystems, PE Sciex, and Celera, on the one hand and Waters, Micromass, and Bio-Rad Laboratories on the other.


The price tag for all of this? “Five to six million,” Naylor said. But if you have the money, he thinks starting a functional proteomics company is worth a shot. Although the field is still in its infancy, it’s “rapidly maturing, and there’s certainly room for a very nimble, well thought-out company to make some significant contributions in the space of differential and functional proteomics.”

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