Project Summary: Core A The DDBTRCC Proteomics Core A is coupled to the Johns Hopkins University (JHU) School of Medicine Mass Spectrometry and Proteomics Facility and provides DDBTRC Center investigators faster access to the services of the JHU Core, a designated Core Proteomics Specialist with whom to work, a specific biostatistician/bioinformatician for post identification/quantification data analysis, all at a reduced cost. The Proteomics Core uses mass spectrometry coupled to multi-dimensional separations by column chromatography or gel electrophoresis to identify, quantify or characterize proteins and their post-translational modifications, expressed in well characterized protein fractions from cells, tissues or body fluids. Techniques such as isobaric mass tag labeling (TMT, tandem mass tags, or iTRAQ, isobaric tag for relative and absolute quantitation) and stable isotope labeling of amino acids in cell culture (SILAC), as well as non-labeling methods (MuDPIT, multi-dimensional protein identification technology) are available for quantifying relative differences in protein expression and post-translational modifications, such as acetylation, AMPylation, citrullination, glycosylation, phosphorylation, nitrosation, proline hydroxylation, ubiquitination and novel cleavage sites. For determining the amount of specific proteins, the Core offers recently established targeted proteomic methods, such as Absolute Quantification (AQUA) and Protein Standard Absolute Quantification (PSAQ) methods. In addition, the Core offers high resolution mass and fragmentation analysis of intact proteins, a top down approach to characterize proteins and their modifications. All Core services include pre- and post-analysis consultation on sample preparation; a Core Proteomic Specialist assigned to receive and analyze the samples; proteolytic digestion, peptide extraction, labeling and fractionation; nano-liquid chromatography separation coupled to tandem mass spectrometry analysis; database searching, data analysis and interpretation, compiled results reports; and educational programs through core presentations and technical workshops. A biostatician/bioinformatician is available when more in depth statistical and ontological analyses of the proteomic results is needed. For DDBTRCC investigators who wish to perform their own analysis the Core provides access to proprietary software and equipment, and Core workshops are offered several times a year on operating the Core MALDI mass spectrometer. 18 current Members, 6 Associate Members and a total of 30 Core Center investigators from our entire funding period have used the Proteomics Core and 51 manuscripts are attributed to this Core.
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