The National Institutes of Health awarded at least $356.5 million in more than 1,000 grants for proteomics research in fiscal 2009, including nearly $55 million in stimulus funding, according to an analysis by ProteoMonitor of an NIH database (see related story, this issue).
The following outlines the 10 proteomics projects that received funding last year:
Project Name: The Uniprot Protein Sequence and Function Knowledgebase
Principal Investigator: Rolf Apweiler
Institution: European Molecular Biology Laboratory
Amount for FY 2009: $4,999,953
Funds further development of and support for UniProt. Specifically, the UniProt Knowledgebase will be developed and maintained as the central database of curated protein sequences with annotations of sequence and functional information. The UniProt Archive will also be developed and maintained, and the UniProtKB entry history server will be created "to ensure comprehensive coverage of all protein sequences and their annotation history," according to the abstract. Other efforts include development of the UniProt Reference Clusters; user-friendly interfaces; tools for simple and complex queries and retrieving large datasets; and providing the flexibility and adaptability "needed to be responsive to the changing needs of the scientific community."
Project Name: Laboratory of Proteomics and Analytical Technologies
Principal Investigator: Larry Arthur
Institution: Science Applications International Corp.
Amount for FY 2009: $4,517,214
According to the abstract, the Laboratory of Proteomics and Analytical Technologies of the National Cancer Institute-Frederick has undergone a restructuring "to provide more effective service to the research community." The laboratory continues to develop methods for improving proteomics analysis. "It has been agreed that the 400 MHz NMR will be removed from LPAT and placed within a centralized nuclear magnetic resonance facility. … LPAT's role in maintaining and operating this instrument is still to be determined," the researchers said in the abstract.
Project Name: Measuring Cancer Biomarker Candidates by Targeted MS and Ab Enrichment
Principal Investigator: Steven Carr
Institution: Broad Institute
Amount for FY 2009: $2,833,858
Funds a project to assess the robustness of a high-throughput mass spectrometric technology platform for the quantitative measurement of multiple candidate biomarker proteins in complex biological samples. Assays will be developed for 300 candidate protein biomarkers. The assays will be used to measure biomarker levels in 200 selected cancer samples and 200 control plasma samples at three different laboratory sites using two different MS platforms. "The results will characterize the quantitative reproducibility of the assay methodology within and between laboratories and over time," according to the abstract. Standardized reagents will also be developed so that the assays can be implemented in other laboratories.
Project Name: Biomarkers of Exposure to Hazardous Substances
Principal Investigator: Bruce Hammock
Institution: University of California, Davis
Amount for FY 2009: $2,588,040
Using an epidemiological approach, investigators will examine the effects of transporting hazardous materials from toxic waste sites. Immunochemical, cell-based, and other systems will be used to detect biomarkers. "The investigators are expanding the use of transcriptomics, proteomics, metabolomics and integrated bioinformatic technologies to discover new mechanisms of action of hazardous materials and biomarkers for their action," according to the abstract.
Project Name: Effects-related Biomarkers of Environmental Neurotoxic Exposure
Principal Investigator: Harvey Checkoway
Institution: University of Washington
Amount for FY 2009: $2,4158,020
The project focuses on "biomarker applications for investigations of adverse effects to human health and the environment from neurotoxic chemicals, primarily metals and pesticides," according to the abstract.
Project Name: A Proteomics Research Resource for Integrative Biology
Principal Investigator: Richard Smith
Institution: Pacific Northwest National Laboratory
Amount for FY 2009: $2,341,594
According to the abstract, the resource center is focused on developing and integrating new proteomic technologies "for biological applications, disseminating the new technologies, and training scientists in their use." The primary technology objectives are to develop and apply an integrated set of biological methods, new analytical technologies, and associated computational and informatics tools, "for much more rapid, quantitative, sensitive, and comprehensive proteomics measurement applications than presently possible."
Project Name: Towards Mega-throughput, Label-free Genomics and Proteomics: Revolutionizing Micr[oarrays]
Principal Investigator: Aydogan Ozcan
Institution: University of California, Los Angeles
Amount for FY 2009: $2,310,000
The researchers aim to create the "next generation of microarray technologies to achieve an unprecedented mega-throughput." Specifically, they hope to achieve a throughput of greater than 120 cm2/sec, or greater than 4.5 million spots/sec, "which constitutes a speed improvement of [greater than] 3 orders of magnitude when compared to the state of the art," they said in the abstract.
Project Name: Complete Human Peptide and MRM Atlas
Principal Investigator: Lee Hood; Robert Moritz
Institution: Institute for Systems Biology
Amount for FY 2009: $2,274,767
Supports the creation of a multiple-reaction monitoring atlas. At the end of the project, the atlas would have at least four peptides for each of the estimated 20,000 to 25,000 protein-coding genes in the human proteome. It would also include verified rapid and accurate MRM-based mass spec assays for identifying and quantifying any proteins in the human proteome [See PM 10/23/09].
Project Name: Proteogenomics for Organ Transplantation: Prediction, Diagnosis, Intervention
Principal Investigator: Michael Abecassis
Institution: Northwestern University
Amount for FY 2009: $2,214,645
According to the abstract, "there is a pressing medical need for a minimally invasive, objective metric of optimal immunosuppression to monitor therapy and insure long-term success," as well as a need for "a sensitive metric of early, non-immune renal injury that pre-dates creatinine elevations and allows individualized therapeutic interventions before irreversible renal damage." The investigators aim to validate proteogenomic-based peripheral blood biomarker panels in a "serial and prospective monitoring strategy" in kidney transplant patients. Another goal is a prospective blood and biopsy-monitor study in liver and heart transplant recipients using the biomarker panels they discover and validate.
Project Name: Computational Biology Bioinformatics, Imaging & Proteomics Research-RCMI
Principal Investigator: Robert Taylor
Institution: Howard University
Amount for FY 2009: $2,164,002
Supports the enhancement and development of Howard University's Proteomics Core Facility; Biomedical Imaging Core Facility; and the Center for Computational Biology & Bioinformatics.
Source: National Institutes of Health