The proteomics and lipoprotein characterization core (Core B) will provide the powerful tools of modern mass spectrometry and complex data set analysis to Program Project Grant (PPG) investigators. The Core will also provide lipoprotein isolation, and measurements of lipoprotein particle concentration and size using calibrated ion mobility analysis. The Core will permit structural identification and quantitation of lipoproteins including remnant lipoprotein particles (RLPs), as well as VLDL, LDL and HDL, and measurement of lipoprotein particle number of these lipoprotein classes using calibrated ion mobility analysis. Core personnel are proficient in liquid chromatography-electrospray ionization-MS/MS analysis (shotgun proteomics) of complex biological mixtures of proteins, with a particular emphasis on the lipoprotein proteomes and on the quantification of their protein cargo using targeted LC-MSMS analysis. The Core Director established precise methods for quantitation of HDL proteome and applied them to quantification of the HDL proteome in large translational studies and will apply the same methods to other lipoprotein classes through Core B. The unique calibrated ion mobility analysis method measures HDL particle number and 5 subspecies of HDL particles, as well as proatherogenic particles like RLPs, and small dense LDL. We anticipate that all investigators will take advantage of these capabilities. In addition to providing instrumental capabilities and bioinformatics tools, Core B staff will provide consultation and collaboration on the application of mass spectrometry and lipoprotein particle concentration measurements to the Program Project, and integration and analysis of complex datasets. This will include development of new analytical methods targeted at achieving the research objectives of the Program?s investigators. Core B will optimize the efficiency and cost-effectiveness through which these services are provided to PPG investigators by providing a central laboratory. This avoids the need for individual PPG investigators to maintain the required instrumentation in their own laboratories, avoids the high cost of commercial mass spectrometric services, and will ensure consistency between analyses for different project sites (Seattle, St. Louis, and New York). By centralizing and standardizing procedures, Core B will provide a common set of analytical tools that will lead to a unified understanding of molecular mechanisms involved in the physiologic and pathophysiologic processes of diabetic vascular disease.
