Proteomics Core

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Introduction, Goals of Core, Summary of Progress, and Relationship to JHUSOM Mass Spectrometry Core. The Proteomics Core A of the Hopkins DDBTRCC is a part of the larger institutional Mass Spectrometryand Proteomics Facility at Johns Hopkins School of Medicine. This facility is a state-of-the-art Core with highly sophisticated, rapidly evolving, expensive equipment and approaches, made available to all Hopkins investigators due to institutional investments that far exceed what a single investigator could afford in either equipment or the time necessary to gain expertise in areas that are used only sporadically in their studies. The Core couples mass spectrometry to one (1D) and two (2D) dimensional separations by column chromatography or gel electrophoresis to identify, quantify or characterize proteins in complex protein extracts, fractions, gel bands or spots. DDBTRCC investigators have access to all facility expertise and services. The partnership between the Proteomics Core A of the Hopkins DDBTRCC and the JHUSOM Mass Spectrometry Core was designed with the goal of making available to Center Investigators the ability to rapidly resolve and identify proteins of interest from complex mixtures, as well as identifying single proteins as part of protein-protein interactions. The specific goals of this Core are to help Center Investigators identify proteins that are differentially expressed in small intestine, colon, liver and pancreas normally or in diseases of these organs, track interactions with binding partners during changes in signal transduction, identify proteolytic cleavage sites and map post-translational modifications. These goals have been admirably met, with Center Investigators succeeding in each of these areas as well as in discovery projects in which proteins altered in expression in Gl diseases have been identified. This partnership provides Center Investigators access to all our mass spectrometry and proteomics services at a more rapid turnaround than usual and at a reduced cost (sees method of charge-back). Plus, importantly, there is a technical expert assigned to the DDBTRC Center whose job is to understand what our Investigators are trying to achieve, to help plan experimental strategies, design methods of sample preparation, review the generated data, advise on approaches for bioinformatic analysis of the results to help direct areas in need of validation, and assist in training postdoctoral fellows and students via the formal courses offered by the Proteomics Core. This preferential treatment has been a very important aspect of the DDBTRC Center, because it not only has accelerated access of sample handling but more importantly has increased the probability of successful data generation, assisted greatly in determination of ways to validate the data sets, and aided in use ofthe information to move the Investigators' projects ahead. The JHUSOM Mass Spectrometry Facility is administered by the Department of Biological Chemistry via a scientific advisory board and is supported by yearly input from the JHUSOM Basic Science Departments fund from the Dean of the School of Medicine. The Basic Science Directors oversee all cores and advise or request funds from the Vice Dean of Research for operational needs of this core. The Hopkins DDBTRCC is one of four groups that has raised funds via Core applications to partially support the JHUSOM Mass Spectrometry Facility. The others are: International Health Nutriproteomics Center Gates Foundation Grant, Cancer Center NCI Support Grant, Novel Therapeutics/HIV-Associated Cognitive Disorders NIMH Gran (Fig. 1). All Grant/Contract principal investigators interact directly with the Core Director and the Advisory Board. Importantly, the DDBTRC Center involvement in the JHUSOM Mass Spectrometry Facility has encouraged rapid development of techniques to deal with membrane proteins, which is the interest of most Center Investigators. This is an indication of the importance for our Core Center of being part of this arrangement. This is one ofthe ways Center Investigators have been encouraged to use this resource. Each supporting Center (in our case DDBTRCC) clarifies the needs of its investigators to Dr. Cole who decides on services to be developed/provided. In almost 6.5 years of interactions, our Mini Center Core PI has worked with the JHUSOM Mass Spectroscopy Facility and Core A Director, R Cole with no disagreements. Needs of the Mini Center have been met and services needed by our Center have been considered and satisfied. This has been a remarkably positive and satisfying relationship. Should any issues that cannot be resolved by interactions between the Core Center and R. Cole, arise, a mechanism is in place in which the Core Center PI can address the JHUSOM Mass Spectroscopy and Proteomics Center Advisory Board over the disagreement. However, it is not anticipated that this mechanism will be required/used as there are no issues of disagreement in Core activities/services that are currently being considered.