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Mass spectrometer weighs in as proteomics breakthrough

Assists in studies of microbes, viruses

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September 03, 2002 Share This!

RICHLAND, Wash. — A faster, more thorough mass spectrometry method for identifying proteins may significantly advance the technology infrastructure required to comprehend the role proteins play in cellular function and disease development. Already, the one-of-a-kind system, developed at the Department of Energy's Pacific Northwest National Laboratory, is beginning to provide new insights into how microorganisms gobble carbon out of the atmosphere and the role proteins play in a virus known to cause blindness.

PNNL researchers have constructed the first-ever high-throughput, or extremely fast, Fourier-transform ion cyclotron resonance, or FTICR, mass spectrometer. The system will provide an unprecedented ability to thoroughly identify and characterize proteins. Measurements of protein abundance levels at different times are key to understanding on a molecular level cellular function and disease progression, treatment and prevention.

"Our system's advantages are simple yet significant. We can identify a larger number of total proteins and more of the less abundant proteins, and we can do both more quickly than current approaches," said Richard D. Smith, PNNL principal investigator. "These advances mean we can get to the answers behind major scientific questions more efficiently and knowledgeably, such as how a disease progresses, and what can be done about it. The end goal is to gain the insights needed to solve these problems."

Called PROMS for Protein Mass Spectrometer, the instrument is a 9.4 tesla FTICR system manufactured by Massachusetts-based Bruker Daltonics Inc. that PNNL researchers extensively modified with hardware and software tools that enable identification of an extremely wide range of proteins.

The system has an exceptional capability for identifying proteins that exist in small quantities-with sensitivities up to 100 times greater than other methods. While small in quantity, these low-level proteins often play important roles in key cellular functions, such as cell regulation, and can be important in disease development. If these low-level proteins aren't identified and can't be measured, scientists have an incomplete understanding of how cells function.

PNNL researchers have already begun using PROMS to characterize the proteomes of three microorganisms of interest to DOE. (A proteome is the collection of proteins expressed by a cell under a specific set of conditions at a certain time.) Microbes being studied include: Rhodopseudomonas palustris, whose intricate metabolic pathways may enable the microbe to sequester carbon from the atmosphere; Shewanella oneidensis MR1, which is able to transform certain pollutant metals and radionuclides into stable or harmless forms; and Deinococcus radiodurans, which is well-known for its ability to survive doses of radiation lethal to humans.

"We want to learn from these microorganisms in hopes of leveraging their unique capabilities to address key environmental challenges," according to Marv Frazier, director of the Life Sciences Division and acting director of Medical Sciences within DOE's Office of Science. "For example, if we learn what proteins are involved in the function of pulling carbon from the atmosphere, could we use R. palustris as a natural source of carbon sequestration to reduce global warming? These are fundamental questions we'll now be able to address in a more thorough manner."

PNNL scientists also are characterizing the proteome of cytomegalovirus, known for causing retinitis, a blinding condition, in hopes of determining which proteins cause the infection and devising ways to counteract it.

In addition to its comprehensiveness, the PROMS capability also is faster than another widely used proteomics mass spectrometry technique called tandem mass spectrometry, or MS-MS. While MS-MS requires the generation of one spectrum, or data set, for each and every identified protein, with each and every sample analyzed, PNNL's approach can identify many proteins from one spectrum after initial validation using MS-MS. After validation takes place, the system uses biomarker tags to avoid the tedious MS-MS step. The time required for analysis with PROMS is thus shortened considerably with results produced 10 to 100 times faster.

The PROMS system is housed in the William R. Wiley Environmental Molecular Sciences Laboratory, or EMSL, a DOE scientific user facility at PNNL.

The Department of Energy's Office of Biological and Environmental Research provides operating funds for EMSL and also funded development of PROMS under a special capability development program.

Business inquiries on PNNL research and technologies should be directed to 1-888-375-PNNL or e-mail:

Tags: Fundamental Science, EMSL, Mass Spectrometry and Separations, Proteomics

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