Development of New Approaches and Methods in Biological Mass Spectrometry and Proteomics.

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Development of New Approaches and Methods in Biological Mass Spectrometry and Proteomics. Our research program pertains to the development of new approaches and new methods in biological mass spectrometry and proteomics as well as their applications to solve biological questions. Our research is highly multidisciplinary involving the fields of mass spectrometry, bioinformatics, separation sciences and various areas in the biological and biomedical sciences. Despite major technical advances in mass spectrometry and associated technologies and the publication of first drafts of the human proteome, there are still many unresolved issues that needed to be addressed to solve complex biological questions. Remaining challenges include the detection of low abundance proteins and the full characterization and quantification of post-translational modifications. In this grant application we propose a number of innovative strategies to address these specific issues by using state-of-the-art techniques and instrumentation available in our laboratory (LTQ Orbitrap Elite, Q-Exactive , 4000 Q-Trap). An important component of this research will involve preparation of synthetic peptides as standards and the development of bioinformatics tools to facilitate the analysis of complex mass spec data. (e.g., protein identification based on accurate mass and LC retention time; identification from MS/MS spectra containing more than one peptide). In order to identify the full extent of post-translational modifications of proteins we will use “top-down” and “medium-down” approaches in combination with traditional “bottom-up” proteomics. To do this we will use new enzymes and new conditions to achieve optimal size for analysis. This research will expose students to a variety of techniques and will be a fertile environment for their training.