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Texas Universities Adding 10-Plus New Mass Spectrometers with $10.4M in CPRIT Funding

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By Adam Bonislawski

The Cancer Prevention Institute of Texas this week awarded $10.4 million in funding for new mass spectrometry core labs at the Baylor College of Medicine and the University of Texas Southwestern Medical Center.

These facilities, along with a new lab under construction as part of Baylor University's Department of Chemistry and Biochemistry, could add more than ten new mass spectrometers to Texas universities, offering a potential bright spot for vendors hurt by the recent slowdown in US academic spending (PM 10/28/2011).

The new labs are: a proteomics core facility at UT Southwestern funded by a five-year, $4.4 million CPRIT grant; a proteomics and metabolomics core at BCM funded by a five-year, $6 million CPRIT award; and an –omics research laboratory at Baylor University funded internally by the school.

At UT Southwestern, the researchers aim to develop a combination of shotgun and targeted proteomics capabilities, Hamid Mirzaei, assistant professor of biochemistry and principal investigator on the school's CPRIT grant, told ProteoMonitor.

To that end, the lab plans to acquire "some TOF [mass spec] instruments and some trap instruments like a [Thermo Fisher Scientific] Orbitrap or Q Exactive" as well as "triple-quads for doing [selected-reaction monitoring] work and targeted mass spectrometry," he said.

The plan, he added, is to acquire around four new instruments at the start, and then add additional instruments "as the need increases" throughout the grant's five-year term.

Mirzaei declined to say what make of instruments the facility was leaning toward, noting that the researchers have sent test samples out to several companies and "are waiting for the results to come back before making any decisions."

"There are quite a few competitors, and they all seem to have significantly improved their platforms, so it's time to reevaluate them," he said.

Touradj Solouki, who is heading development of the new Baylor –omics lab, likewise told ProteoMonitor that his team was still evaluating what instruments it hoped to purchase, adding that they would likely buy three or four new mass specs. He mentioned the new Thermo Scientific Orbitrap Elite as a possibility, and noted he was also interested in adding ion mobility and MALDI-imaging capabilities to the lab.

Dean Edwards, professor in the Departments of Molecular and Cellular Biology and Pathology at BCM and, with his colleague Jun Qin, co-principal investigator on that institution's CPRIT grant proposal, told ProteoMonitor that the researchers had settled on a Thermo Scientific Orbitrap Elite for the new proteomics and metabolomics core. The facility will also obtain two Agilent 6490 triple quadrupole machines for targeted proteomics and metabolomics work – one purchased with funds from the CPRIT grant and the other with philanthropic funds from the Albert & Margaret Alkek Foundation.

The lab will also purchase an Aushon Biosystems 2470 Arrayer for printing reverse phase protein microarrays, Edwards said. RPPA technology offers better sensitivity and higher throughput than targeted mass spec approaches like SRM assays, he said, making it a good choice for the translational research he expects the facility will focus on.

With RPPA assays "you don't need to do prefractionation steps, and with good quality antibodies you can detect very low abundant proteins," he said. "And if you do dilution curves you can get pretty wide dynamic range and make these assays pretty quantitative."

The facility also plans to purchase liquid handling equipment to automate the RPPA process, Edwards said, "because our goal is to do large clinical translational studies. So an investigator will be able to handle 300, 400, even 1,000 tumor samples if they need to."

The BCM facility will be part of the school's new Alkek Center for Molecular Discovery and will apply proteomics and metabolomics to the study of multiprotein complexes with a particular focus on studying cancer drug resistance, Edwards said.

He added that, while the first year of the grant will go primarily toward equipment purchases, the following four years would provide roughly a million dollars per year to support the efforts of individual cancer researchers at BCM.

"We've identified 45 cancer investigators [who] said they had a need for these kinds of proteomic and metabolomic projects, and the [CPRIT grant] is going to provide much of the funding for these investigators to do their research," he said. "We're going to have an internal request for applications from these investigators, and they will submit their projects, and there's a committee of senior faculty who will decide how to distribute the funds."

Given its CPRIT funding, the UT Southwestern facility will similarly have a cancer focus, with research interest divided more or less equally between investigations of basic cancer biology and cancer biomarker work, Mirzaei said.

The Baylor –omics lab will also pursue cancer biomarker research, with markers in non-invasive samples like saliva being of particular interest, said Solouki.

All three facilities will serve investigators studying other diseases as well, the scientists said. Establishment of the UT Southwestern facility, Mirzaei noted, was driven by growing demand for proteomics tools by the school's researchers that made a devoted proteomics center desirable.

Proteomics had been housed with the institution's Protein Technology Center, "but proteomics has outgrown" that center, he said.

Edwards likewise noted strong demand for proteomics tools among BCM scientists.

"We did a survey of Baylor investigators before submitting this grant, and there are so many investigators that have a need to use one of these – either metabolomics, RPPA, or mass spec-based proteomics – that we'll be 100 percent busy," he said.


Have topics you'd like to see covered in ProteoMonitor? Contact the editor at abonislawski [at] genomeweb [.] com.

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