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ABRF Panel Addresses Challenges of Implementing Mass Spectrometry into Core Labs

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MEMPHIS, Tenn. — A professor of chemistry at Washington University, Michael Gross is one of three people who run the mass spectrometry facility at the National Institutes of Health's National Center for Research Resources at the school.

The facility is housed in three laboratories, including one located in the chemistry department that Gross oversees. The two remaining laboratories, including one devoted entirely to proteomics, are based in the university's School of Medicine.

Gross oversees more than 10 mass specs ranging from ion trap FTICR instruments to garden variety ion trap platforms. With support from NIH's high-end instrument grants, the university also recently purchased a 12 Tesla FTICR platform and a MaXis UHR-TOF system, both from Bruker.

While the MS facility in the chemistry department has been able to secure most of its instruments through NIH HEI and shared-instrument grant funds, funding from the university has not been as easy to get. In contrast, he said, the two labs in the School of Medicine have been funded primarily through Washington University, due to the clinical nature of the work being conducted in those labs.

While many other core-facility directors struggling to find financing for new instrumentation would gladly trade places with Gross, his example demonstrates the challenges that shared facilities face, and this week at the annual conference of the Association of Biomolecular Resource Facilities, a workshop was held to address some of the problems that directors such as Gross may encounter in implementing new mass-spec technologies in a core lab and what can be done to work around them.

In addition to Gross, Sarka Beranova-Giorgianni and Gary Nelsestuen spoke during the session.

Beranova-Giorgianni is associate director of the Charles B. Stout neuroscience mass-spectrometry laboratory at the University of Tennessee Health Science Center, where she is also an assistant professor in pharmaceutical science. Nelsestuen is director of the center for mass spectrometry and proteomics at the University of Minnesota, where he is also a professor of biochemistry.

Because of the different sizes and work that each lab does, the concerns and obstacles faced by each have some variance, but each also shares common experiences. At the top of the list is funding. Each of the three speakers said that in large part, they have relied on various NIH funding mechanisms. But Beranova-Giorgianni and Nelsestuen have also relied on other sources.

For example, an LC-nanoESI-QTOF that Beranova-Giorgianni's lab purchased in 2002 was paid for with individual research grants, she said. And an LC-nano ESI LTQ and a MALDI LTQ were bought in 2005 with an NIH SIG grant totaling $500,000 and funds generated by the trade-in of an existing instrument.

Nelsestuen, meanwhile, has used a patchwork approach to pay for the 15 instruments in his lab used for proteomic and metabolomic research with awards from the National Science Foundation; state grants; Hatch grants from the US Department of Agriculture; the NIH; and funds from the $6.1 billion settlement reached in 1998 between the tobacco industry and Minnesota and that state's Blue Cross Blue Shield insurance plan.

Also used were funds that became available when certain earmark items were dropped from the federal budget, he said.

But it isn't just money for instrument purchases that can be challenging, the presenters said. Finding funds for personnel to run the instruments has often been an issue. When Nelsestuen first joined his facility in 1998, there was no source of regular funding for new hires, resulting in a perpetual staff shortage and high turnaround, he said.

That didn't change until 2004 when the university started an initiative for proteomics and provided $500,000 in funding annually. His lab now has five full-time staff and four part-time staff.

Last year, that amount was raised to $700,000, but, because it is subject to the school's overall financial state, the amount can be lowered.

At UTHSC, Beranova-Giorgianni also said that her facility went through two years when it lost technical support staff due to a lack of support from the school, although that has recently changed.

Teach and Recruit

During the ABRF workshop, the presenters also spoke about the roles their laboratories play within their universities and the surrounding research communities, and factors that play into what instruments they decide to purchase.

At Washington University, the three labs work collaboratively, on many projects, share instrumentation, and teach graduate students and medical scientists in mass spectrometry, though one of the mass-spec labs in the medical school is focused on lipidomics work and the other specializes in proteomics.

Similarly, Nelsestuen and Beranova-Giorgianni said training and education are a large part of their facilities' responsibilities. At the University of Minnesota, Nelsestuen offers bimonthly three-day workshops to use the instruments and helps researchers from around the university to plan their research projects.

The Stout lab at UTHSC is also involved in teaching graduate students and is in the process of designing a course specifically on proteomics, Beranova-Giorgianni said.

When choosing an instrument, all three presenters said that they try to anticipate the evolving needs of researchers. In deciding to purchase an LC-nano ESI LTQ and MALDI LTQ instruments, for example, Benanova-Giorgianni said that her lab saw that there "would be a switch from protein identification from gels to protein identification in complex mixtures.

"We try to identify future directions” in the work of the researchers, she said. "That influences our decisions."

And Gross' lab bought its Bruker instruments to address what he said is a growing number of applications for top-down proteomics, such as work directed at post-translational modifications, he said.

But along with new instrumentation, another factor is whether they have the personnel and expertise to run instrument and, if not, would they be able to hire someone who would, Nelsestuen added.

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