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

生物质谱学和蛋白质组学的新途径和新方法的发展。我们的研究项目涉及生物质谱学和蛋白质组学的新途径和新方法的发展，以及它们在解决生物学问题方面的应用。我们的研究是高度多学科的，涉及质谱学、生物信息学、分离科学以及生物和生物医学科学的各个领域。*尽管在质谱学和相关技术方面取得了重大技术进步，并公布了人类蛋白质组的初稿，但仍有许多尚未解决的问题需要解决，以解决复杂的生物学问题。剩下的挑战包括低丰度蛋白质的检测以及翻译后修饰的充分表征和量化。*在这项赠款申请中，我们提出了一些创新战略，通过使用我们实验室提供的最先进的技术和仪器(LTQ Orbitrap Elite、Q-Exactive、4000 Q-Trap)来解决这些具体问题。这项研究的一个重要组成部分将涉及作为标准的合成多肽的制备和生物信息学工具的开发，以促进复杂的质谱学数据的分析。(例如，基于准确的质量和LC保留时间的蛋白质鉴定；根据包含不止一个肽的MS/MS光谱鉴定)。为了确定蛋白质翻译后修饰的全部范围，我们将使用“自上而下”和“中下而下”的方法，并结合传统的“自下而上”蛋白质组学。为此，我们将使用新的酶和新的条件，以达到分析的最佳大小*。*这项研究将使学生接触到各种技术，并将为他们的培训提供一个肥沃的环境。

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.