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ABI - Northeastern Univ Collaboration Moves into Protein Separation Science

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Applied Biosystems has broadened the scope of its technology partnership with Northeastern University chemist Barry Karger, the company said last week.

In April, ABI announced that it had licensed vacuum deposition technology from Karger’s laboratory for use in MALDI-TOF analysis of proteins. The new phase of the relationship will allow researchers from ABI and Karger’s lab to interact much more closely on a wider variety of issues in protein separation science, said Steve Martin, director of ABI’s proteomics research center in Framingham, Mass.

“Sample prep is a huge bottleneck in proteomics today,” Martin said. “My objective is to come up with connected, integrated systems [that accelerate sample prep], and we’re working with Barry to build prototype equipment,” he said.

Martin said that researchers from Karger’s lab would study ways of seamlessly connecting capillary electrophoresis (CE) and liquid chromatography (LC) systems with Karger’s vacuum deposition interface. The interface is used specifically for arraying peptides or proteins on to MALDI targets in ABI MALDI-TOF mass spectrometers.

In addition to interfacing MALDI with CE and LC systems, Martin said researchers in Karger’s lab would investigate new types of labeling chemistries and separation media, such as chromatography packing materials, and new methods for integrating these techniques with ABI’s new MALDI-TOF/TOF mass spectrometer, which ABI has said it will begin shipping by the end of the year.

ABI, which also manufactures chromatography packing materials and LC separation systems, will provide funding and ABI equipment to Karger’s lab, Martin said, although he would not say whether the MALDI-TOF/TOF instrument was included. Graduate students from Karger’s lab would also work in ABI’s laboratories, added Martin.

ABI has licensed an isotopic-labeling technique from the University of Washington, developed in Ruedi Aebersold’s lab, for differentially labeling peptide fragments, and has a research partnership with Millipore in sample prep techniques.

In an inteview several weeks ago, Martin said ABI’s strategy is “to invest in and focus our efforts on where we can bring a factor of 10 or more improvement to proteomics,” in a manner analogous to the contribution of the ABI 3700 instrument to genome sequencing.

Karger, the director of the Barnett Institute of Chemical and Biological Analysis at Northeastern University in Boston, was not immediately available for comment. According to the university, his research covers a broad range of separation technologies, including microseparation methods, capillary electrophoresis, DNA sequencing with replaceable polymer matrices, functional genomics, drug screening by CE/MS, multichannel microchip - mass spectrometry, and laser-based analysis.

Scientists at ABI’s Framingham location, including Martin and Marvin Vestal, who both worked for PerSeptive Biosystems before it was acquired by PE in January 1998, first began interacting with Karger three or four years ago, primarily at scientific conferences, Martin said. Two years ago, the company began evaluating the vacuum deposition technique, which led to the licensing agreement announced in April. The two groups are also located within a 30-minute drive of each other.

Martin said the collaboration allows ABI to access Karger’s expertise without having to build a research group internally at added cost to time and resources. “We can’t be experts in all areas,” he said.

— JSM

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