Development of new and innovative strategies in biological mass spectrometry and proteomics

我的研究项目旨在开发蛋白质组学研究的创新技术和新方法，以发现广泛生物系统中的新生化机制。蛋白质组学的最终目标是充分表征细胞中的所有蛋白质。由于蛋白质组的复杂性，特别是在高等生物中，从分析的角度来看，蛋白质组学是一个非常具有挑战性的问题。这是由于蛋白质的多种形式和它们在细胞中存在的广泛动态范围。研究蛋白质组最有力的工具是质谱（MS）及其相关技术。质谱仪设计的最新进展为开发解决蛋白质组学挑战的新方法提供了新的和令人兴奋的机会。和过去一样，我们的研究项目将是高度合作的，涉及生物学家、生物化学家和计算机科学家。迄今为止，蛋白质组学的主要策略是所谓的“自下而上”方法，即蛋白质被蛋白酶酶解，产生0.5至3KDa范围内的片段，可以通过质谱分析进行表征。蛋白质的身份是从鉴定的肽片段推断出来的。自底向上的蛋白质组学仍然存在的一个问题是较差的序列覆盖率和错过的翻译后修饰。克服这一问题的一种方法是使用不同的蛋白酶进行消化，但这会导致仪器时间的显著增加，并且难以以自动化和可靠的方式组装所有这些片段。我们将通过设计多蛋白酶消化的新方案来解决这两个限制。与我们的计算机科学家合作，我们将开发新的软件组装所有的肽片段，以获得完整的序列。这对于抗体及其药物偶联物的全面表征尤其重要。然而，我们的目标是将这种方法扩展到复杂的蛋白质混合物中。与这些研究并行，我们将使用新的质谱技术进行“中下”测序，即创建和分析3-10KDa范围内的蛋白质片段。这些蛋白质片段将在非标准条件下通过有限的蛋白质水解产生，或者通过针对蛋白质中低频氨基酸的特定化学裂解产生。这些中等大小的蛋白质片段将在ms注射前通过新方法分离，包括翻译后修饰的序列将通过最近可用的技术（如EthcD和UVPD）片段化获得。这也将刺激开发新的和强大的软件来分析这些数据。总之，我们建议开发新的概念和工具来促进蛋白质组学的进步，这将影响生物学研究的几个领域。我们研究项目的多学科性质将为研究培训提供一个刺激和肥沃的环境。

My research program aims at the development of innovative technologies and new approaches in proteomics research to discover novel biochemical mechanisms in a wide range of biological systems. The ultimate goal of proteomics is to fully characterize all proteins in cells. From an analytical perspective proteomics is a very challenging problem due to the complexity of the proteome, especially in higher organisms. This is due to the many forms of proteins and the wide dynamic range in which they are exist in cells. The most powerful tool to study the proteome is mass spectrometry (MS) and its associated technologies. Recent advances in the design of mass spectrometers offer new and exciting opportunities to develop new approaches to tackle the challenges in proteomics. As in the past our research program will be highly collaborative and involve biologists, biochemists and computer scientists. To date the main strategy in proteomics is the so called "bottom-up" approach where proteins are enzymatically digested by a protease to yield fragments in the 0.5to 3KDa range that are amenable for characterization by MS analysis. The identity of the proteins is inferred from the identified peptide fragments. One the remaining problems in bottom-up proteomics is the poor sequence coverage and the missed post-translational modifications. One approach to overcome this problem is to use different proteases for the digestion but this results in significant increase in instrument time and difficulty in assembling all these fragments in an automated and reliable manner. We will address both these limitations by designing new protocols for the multi-protease digestion. With our computer scientist collaborators we will develop new software for the assembly of all the peptide fragments in order to get complete sequences. This is particularly relevant for the full characterization of antibodies and their drug conjugates. However our goal is to extend this approach to complex protein mixtures. In parallel to these studies we will use new MS techniques to perform "middle-down" sequencing, that is creating and analysing protein fragments in the range of 3-10KDa. These protein fragments will be generated by limited proteolysis in non-standard conditions or alternatively by specific chemical cleavage targeting amino acids of low frequency in proteins. These mid size protein fragments will be separated by new methods prior to injection in the MS. The sequences, including the post-translational modifications, will be obtained by fragmentation with recently available techniques like EthcD and UVPD. This will also spur the development of new and robust software for the analysis of these data. In summary we propose to develop new concepts and tools to promote advances in proteomics that will impact several areas of biological research. The multidisciplinary nature of our research program will provide a stimulating and fertile environment for research training. .