A PNNL scientist uses a ThermoFinnigan LTQ mass spectrometer to identify peptides from living organisms such as Salmonella and Orthopox viruses

powerful mass spectrometers enable comprehensive, quantitative, and high-throughput proteome measurements. As a result, scientists can more quickly answer questions of how proteins, and thus cells, operate.

PNNL's high throughput analysis approach is similar to "shotgun" proteomics approaches in that proteins are first cleaved into peptide fragments and then analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify peptides. However, unlike "shotgun" approaches, the results from these initial analyses are used to create a reference database that contains mass and chromatographic elution time information for each peptide; that is, a mass and time tag that serves as a unique two-dimensional marker for subsequent identifications of that particular peptide.

Once a reference database has been created, future samples from the same organism need only be analyzed by high-resolution LC-MS (such as Fourier transform ion cyclotron resonance or time-of-flight) since detected peptides can be identified by comparing mass and elution time characteristics with those in the reference database. This approach not only increases throughput by eliminating the need for routine MS/MS, but also provides greater analytical sensitivity.

These high-throughput analyses create massive amounts of data since a single cell can express many thousands of proteins. PNNL developed the Proteomics Research Information Storage and Management System (PRISM), an easily configurable and scalable capability, to handle these ever-increasing volumes of data. PRISM not only collects data files directly from all mass spectrometers, but it also manages the storage and tracking of these data files and automates data processing to provide both intermediate results and final products.
 

What's Happening …

The Scientific Working Group (SWG), an advisory team composed of scientists with a broad range of expertise in proteomics, bioinformatics and infectious diseases, is pleased to welcome their newest member, John Belisle, Ph.D, an Associate Professor in the Department of Microbiology, Immunology and Pathology at Colorado State University. Another member of the SWG, Thomas Geisbert, Ph.D., and his lab team from Ft. Detrick, MD, were featured in the October 2, 2005 edition of the Washington Post. The article recounts Dr. Geisbert's efforts to develop a vaccine for Ebola.

The Administrative Resource Center for Biodefense Proteomics Research Centers presented at HUPO's 4th Annual World Congress in Munich, Germany. Peter McGarvey, PIR/GU, was the Administrative Center's representative.

Cathy Wu (PIR/GU), Administrative Center and IWG member, was elected to the HUPO Council. She will serve a three-year term beginning November 1, 2005.

Relevant Publications …

Structural genomics of the severe acute respiratory syndrome coronavirus: nuclear magnetic resonance structure of the protein nsP7 - J Virol. 2005 Oct;79(20):12905-13 [PMID: 16188992] The Scripps Research Institute

Inhibition, escape, and attenuated growth of severe acute respiratory syndrome coronavirus treated with antisense morpholino oligomers - J Virol. 2005 Aug;79(15):9665-76 [PMID: 16014928] The Scripps Research Institute

The utility of accurate mass and LC elution time information in the analysis of complex proteomes - J Am Soc Mass Spectrom. 2005 Aug;16(8):1239-49 [PMID: 15979333] Pacific Northwest National Laboratory

Murine macrophage transcriptional responses to Bacillus anthracis infection and intoxication - Infect Immun. 2005 Feb;73(2):1069-80 [PMID: 15664951] University of Michigan

Upcoming Meetings …

Pacific Symposium on Biocomputing 2006: Computational Proteomics Grand Wailea, HI January 3-7, 2006