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Penn to Spend $5 Million to Establish University-Wide Proteomics Core Facility


Not to be outdone by its proteo-centric Ivy League neighbors to the north, namely Harvard, the University of Pennsylvania is embarking on its own effort to build a comprehensive core facility for proteomics research. The university has yet to allocate a specific space for the new 2,500 square foot facility, but has pledged $5 million for the future purchase of 2D gel and mass spectrometry equipment, said Ian Blair, a professor of pharmacology at the university and the director of the core proteomics facility.

Although the new dean of Penn’s school of medicine has yet to decide where to locate the lab, that hasn’t stopped Blair from picking out 2D gel separations and imaging software from Amersham Biosciences and GeneBio, two Applied Biosystems Voyager DE Pro MALDI TOFs, two ABI QSTAR Q-TOFs, and two LCQ Deca ion traps from Thermo Finnigan. “It’s been going through the machinations of getting approval for all of that and almost everything is sorted out except for where to locate it,” he said. “Space in medical schools is a major issue, and hopefully that’s going to get resolved in the next two weeks or so.”

Although Blair said he recognized the need for Penn to support a dedicated proteomics core lab about 18 months ago, the current proposal took shape earlier this year after Penn’s Cancer Center, Genomics Center, and the Abramson Family Cancer Research Institute agreed to help support and administer the research facility. “It was pretty clear to me that we needed to increase our capabilities in the area of proteomics, so I proposed to the dean that he invest some money in this area because it would help not only this program but other people at Penn,” said Blair.

The proteomics center at Penn also hopes to tap into a National Heart, Lung, and Blood Institute grant for developing a multi-disciplinary proteomics technology center, according to Blair. The grant is somewhat unusual because of its focus on technology development and extended time scale — the successful applicant will receive $15 million over 7 years — but Blair thinks the university’s chances are good. Last year, NHLBI awarded Penn a $15 million SCOR (Specialized Center for Research) grant, and Penn’s success may give it an edge over other applicants, Blair said.

If that money comes through, Penn would invest in a Thermo Finnigan TSQ Quantum, a high-end benchtop triple quadrupole mass spectrometer, among other equipment purchases, Blair added. “The main reason for that is that we’re developing some novel quantitative proteomic strategies with high sensitivity,” he said, referring to stable isotope labeling technology under development at the university.

Blair said the added funding also would help Penn apply techniques for studying single-cell proteomes developed by Jim Eberwine, a researcher in the department of pharmacology who published his RNA-amplified protein detection technique in May 2001 in the Proceedings of the National Academies of Science. Blair added that he hopes to apply to proteins his own research into modifying DNA with lipid peroxide.

Access to the proteomics facility, once it finds a home, will be determined by an advisory committee that will give each specific proposal a priority score, Blair said. “This was designed because we have two different mechanisms of funding. You have the medical school which is primarily NIH funded, and the schools of engineering and arts and sciences, which is primarily [funded through] teaching appointments,” he said. “It’s trying to play to both constituencies with equal access.”

Blair, who for 12 years ran the mass spectrometry lab at Vanderbilt now under the direction of Richard Caprioli, said his budget will allow him to hire a scientist to oversee the day-to-day operations of the proteomic core facility, as well as several support staff. “There’s a frightening need for it in a place like this,” he said. “I have a vision of 1,000 investigators suddenly descending on me, wanting to run samples!”


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