Development of a Proteomics Core at Dartmouth


Biomedical research is rapidly entering the post-genomic era as we turn from analyzing expression of individual genes or the entire suite of expressed genes (“genomics”), to the analysis (“proteomics”) of the proteins these genes express (the "proteome") in order to understand the mechanistic basis for normal and pathophysiological processes. Proteomics investigates protein expression and protein:protein interactions on a more global scale than investigations of individual proteins, and includes both changes in levels of expression that might result from alterations in gene expression, as well as post-transcriptional and post-translational modifications to proteins that can fundamentally alter their functional expression independent of gene expression changes.

Proteomics is a major component of four of the five proposed research projects of our COBRE program, as well as a central part of the research of the senior mentors of this program. Dartmouth is in the process of establishing the infrastructure to support proteomics research as the next logical step in its biomedical research plan. Our goal is to develop a fully functional Proteomics Facility Core with a complete series of proteomics-related services. We have begun the process of developing a Proteomics Core within the existing Molecular Biology core facility which has been re-named the Molecular Biology & Proteomics Core. This began two years ago with the acquisition of a Matrix-Assisted Laser Desorption-Ionization Time-Of-Flight (MALDI-TOF) mass spectrometer and an Electrospray Ionization Quadrapole (ESI-Q) mass spectrometer along with 2D gel analysis equipment and other instrumentation. However, to fully function as a viable, cost-effective and cutting edge proteomics core, several other components were still required. These included renovation and expansion of the Facility Core's laboratories, creation within the new space of a protein biochemistry wet laboratory to train and support investigators in the identification, isolation and purification of proteins, acquisition of additional pieces of proteomics support equipment, and support for additional professional personnel for these proteomics services. With the awarding of the COBRE grant and with the commitment of matching resources from Dartmouth, these additional improvements have now been instituted.

Proteomics will be especially important for the development of our mentored faculty to a point of being established, independent, externally funded investigators. Proteomics is clearly going to be one of the major tools of cutting edge research for most biomedical fields over at least the next 5 years, and has been identified as a major need of our COBRE faculty. Thus, we see establishment of a proteomics core as central to our mission within the COBRE grant and also vital to the institution's research enterprise as a whole. The goal for this Core over the period of this grant is to first establish the infrastructure to support proteomics research, and then to support the development and application of these tools to the individual research projects of this COBRE program with the aim that these investigators will be nationally competitive for external funding utilizing advanced proteomics research by the end of this program period. In addition, this Facility Core will continue to provide other vital services to these researchers in the related areas of molecular biology, biochemical analysis, genomics and bioinformatics. These services will be provided in a highly cost-effective way from a single, centrally located facility in the heart of the biomedical research enterprise.

The new Proteomics Core will enable our individual researchers to perform experiments that are too expensive and/or specialized to be included in individual research grants and therefore might not otherwise be possible or practical were these services not centrally available at the institution. Four of the five research projects of this COBRE program will extensively incorporate proteomics based research into their projects over the five-year period of this grant (Drs. Madden, Treadwell, O’Toole, Swiatecka-Urban). The fifth group (Dr. Duell and Co-PI, Dr. Shi), while not applying these tools directly in their research, plan to collaborate with Dr. Treadwell and others in the program, who will use proteomics in their research projects. Drs. Madden, Swiatecka-Urban, O’Toole and Treadwell have already begun to use the Proteomics Core at Dartmouth in their research. The Director of the Molecular Biology & Proteomics Core Facility is Dr. Joshua Hamilton, who is a Professor of Pharmacology & Toxicology at Dartmouth Medical School and also serves as an Co-Associate Director of this COBRE research program. His is also the mentor for Project 5 and a co-mentor for Project 4. Dr. Jack Bodwell is Associate Director of the Core, and has specific expertise in protein biochemistry. Mr. Stephen Bobin is the Manager of the Core and also has extensive expertise in protein biochemistry. Ms. Susan Kennedy serves as the Technical Specialist for proteomics services.

The goal of the COBRE grant is to provide proteomics support in several ways: First, we will use these resources to immediately establish a fully functional Proteomics Facility Core with capabilities to identify, isolate, purify and analyze proteins from a variety of biological systems. Second, we will also immediately establish a protein biochemistry wet laboratory within this Facility Core, which will be used both to train investigators in the tools and methodologies of protein biochemistry and proteomics research, and to support ongoing projects as they identify and analyze proteins in their experimental systems. Third, we will work with the Principal Investigators of this COBRE program beyond the initial training period, to fully develop proteomics approaches that are incorporated in their project plans as outlined in their individual proposals. We plan to develop the basic proteomics facility and services, and the protein biochemistry wet laboratory, within the first year of the grant so that we can begin training investigators in Year 01 and also allow those who are ready, such as Drs. Madden, Treadwell, O’Toole, and Swiatecka-Urban, to immediately have access to proteomics services for their research. We will then add additional functionality, particularly higher level separation and analysis capabilities and higher throughput services, in Years 02-03 of the projects, so that they will be fully capable of in-depth proteomics research in Years 03-05 of the program. This will allow these young investigators to mature their research to a point of being nationally competitive in the application of proteomics approaches within their respective fields of inquiry by the end of this program period.

The principal tools that these investigators will use will be 1D and 2D protein separation and analysis techniques; detection and quantitation of protein:protein interactions; protein sequencing; peptide synthesis, purification and sequencing; and structural analysis of proteins and peptides using ESI-Q and MALDI-TOF mass spectrometry. In addition to these Principal Investigators, the senior mentors of this program also will use proteomics approaches in their research as these services become available. Incorporation of proteomics into these senior investigators' laboratories will both enhance the functionality and use of this Proteomics Core, as well as providing additional expertise and advice to the COBRE Principal Investigators and their laboratories as they develop these same proteomics tools for their own research. Thus, in this way, the mentors will benefit from their participation in this COBRE Program. This new Proteomics Core, within the expanded and renovated Molecular Biology & Proteomics Core, is also expected to significantly enhance the research capabilities of the entire Dartmouth research community.