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UMMS Obtains Tools from Charles River, MBI for New Proteomics Consortium


The University of Massachusetts Medical School has established a proteomics facility that brings together the school's proteomics and mass spectrometry facilities, resources from Charles River Laboratories' old proteomics facility, and bioinformatics tools from the nonprofit Massachusetts Biomedical Initiatives.

The facility, called the Proteomics Consortium, is meant to serve university researchers as well as small local biotechnology companies and other external researchers, the group said. UMMS plans to charge premium rates for external users to either use the facility or contract university researchers to perform certain proteomic services. It plans to charge internal users a fee that covers the costs of reagents and consortium workers' salaries, it said.

"There's a large demand both on and off campus for proteomic services," said James Evans, a UMMS research assistant professor who runs one of the university's two proteomics and mass spec core facilities. "The three groups working together is going to considerably enhance our ability to meet those demands. It will also have an impact on research funding and projects that get carried out here, and it will make it possible for many of the smaller biotech companies to obtain some of the proteomics services."

The Proteomics Consortium, which opened its doors in the first quarter of this year, was created mainly because Charles River Laboratories' proteomic facility, based in Worcester, Mass., had closed last December (see ProteoMonitor 12/10/2004), said Sunny Tam, a former manager of the sample preparation team at Charles River Proteomic Services.

Before it closed down, CRPS had many clients on the U Mass campus, according to Tam, who joined UMMS in January as an associate professor and the director of the Proteomics Consortium's Protein Fractionation Group (see Proteomics Pioneer). CRPS performed a lot of the sample preparation, including sample fractionation, before analysis using mass specs at UMMS.

When Charles River Laboratories decided to close down its proteomics unit because it "hadn't met growth goals," UMMS invited Tam and his associate, Douglas Hinerfeld, who had also worked with UMMS at CRPS, to come on board. The university also bought some protein fractionation and analysis equipment from Charles River and brought it over to the school's Shrewsbury campus.

"It was a nice marriage of sample prep with mass spec, which is the core of [the Proteomics Consortium's] proteomic services," said Tam.

UMMS' mass spec equipment includes a new Waters QTOF Premier mass spec system, a Finnegan LTQ, a MALDI-TOF/ion trap hybrid, triple quads, regular MALDIs, and more, according to Evans. The university decided not to purchase any mass spec equipment from CRPS because the company's mass spec equipment was older and less sophisticated than the university's. The CRPS resources are being used mainly for sample fractionation and sample processing before submission into mass specs.

"In my facility, the mass spec equipment purchase price totals somewhere around $2 million," said Evans.

The Proteomics Consortium's alliance with MBI came about because many U Mass investigators had used the non-profit's bioinformatics services in the past to help build databases, make a website accessible, or perform more sophisticated proteomics database searches. The alliance does not involve any financial arrangement, but is more of a collaborative agreement to enhance exposure of both UMMS and MBI, and to foster intellectual exchange, Tam said.

"Investigators have collaborated with MBI since their inception several years ago, but there was never a formal arrangement until now," said John Leszyk, a research assistant professor who runs a proteomics/mass spectrometry lab at UMMS.

Joseph Gormley, the acting director of informatics and computing resources at MBI, said that his organization offers informatics support to companies and institutions that find it too costly to have in-house bioinformatics facilities. By combining MBI's computing facilities, which includes an IBM eSeries cluster, with UMMS' proteomics facilities, the Proteomics Consortium can offer an attractive package to companies, he added.

"Our alliance with UMMS … brings together two important resources that will help support our existing companies and attract others to the region," said Gormley.

Projects that are currently underway using the UMMS facility include a study that is looking at what proteins are up- or down-regulated or post-translationally modified in a number of eye diseases; a study that is using proteomic approaches to investigate cellular immunity to some of the major pathogens that can be used as bioterrorism weapons; and studies to identify protein biomarkers for cancer, Alzheimer's disease, and type II diabetes.

Leszyk said that the fee charged for outside clients to use the Proteomic Consortium's facilities or to obtain proteomic services would be comparable to fees that are charged by commercial operations.

"Part of the reason of venturing to outside users is that the additional revenue can be used to buy equipment and further grow the laboratories in terms of technical development," said Leszyk. "It's very difficult for academic core facilities to get funding. These facilities need to be supported by the institution, or to have some mechanism of support."

Tam said that the university is not really trying to compete with other proteomics services providers. "We are just trying to leverage what we have and provide the help to both on campus faculty and biotech," he said. "We're helping the local economy by providing equipment. It's a win-win situation."

— Tien Shun Lee (tle[email protected])

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