Novel Technologies for Protein Analysis

蛋白质分析新技术

• 批准号: 9912172
• 负责人: LLOYD M SMITH
• 金额: $ 61.81万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-05-01 至 2023-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9912172
• 关键词: Adoption; Amino Acid Sequence; Base Sequence; Biological; Biology; Cell physiology; Cells; Communities; Complex; Computer software; DNA; Data; Databases; Development; Disease; Effector Cell; Family; Genetic Variation; Individual; Laboratories; Mass Spectrum Analysis; Measurement; Methods; Molecular; Pathway interactions; Post-Translational Protein Processing; Preparation; Process; Protein Analysis; Proteins; Proteomics; Protocols documentation; RNA; RNA Splicing; Research; Research Personnel; Sampling; Scientist; System; Systems Biology; Technology; Visualization software; biological systems; data streams; human disease; improved; infancy; innovation; macromolecule; new technology; novel strategies; open source; response; technology development; tool; transcriptomics

Abstract The primary focus of my laboratory is the development of novel technologies for protein analysis, specifically centered around the concept of the proteoform. Proteoforms, each of which comprises a unique combination of amino acid sequence and post-translational modifications (PTMs), are the primary molecular effectors of cell function. Subtle sequence and PTM differences between proteoforms can completely alter their function and activity. We see comprehensive proteoform-level analysis of biological systems as absolutely essential to understanding their function, for both individual pathways and networks operative within cells, and more globally, to decipher the systems-biology-level dynamics and interactions that control cellular response. For example, one of our projects is to elucidate the interactome between specific nucleic acid sequences and the proteoforms bound to those DNA or RNA molecules. However, today's technology for global proteoform analysis in complex systems is in its infancy, offering both a great challenge and a great opportunity. We seek to develop novel strategies for comprehensive proteoform identification and quantification in complex systems. We envision combining information from multiple data streams, such as transcriptomic data (to reveal splice forms and genetic variation), bottom-up proteomics data (to reveal and localize PTMs), top-down proteomics data (to provide sequence tags for proteoform identifications), and intact mass measurements (to identify and quantify proteoforms, using information from all of the other data streams). Specific projects will develop the following: (1) robust tools for the construction of sample-specific proteoform databases; (2) new strategies for the discovery and localization of PTMs; (3) improved sample preparation, separation, and mass spectrometry methods for intact proteins; (4) synergistic approaches that utilize both intact mass measurements and selected top-down fragmentations to maximize proteoform identifications; and (5) visualization tools for proteoform families that show connections and changes between related proteoforms. We will integrate these methods and data streams together with powerful open-source software and accompanying protocols to make these capabilities widely available, enabling researchers everywhere to gain a deeper understanding of the functioning of their biological systems. We will apply our innovative tools to many cutting-edge projects with numerous collaborators, both because technology development is most meaningful in the context of relevant biological studies and because it will increase the adoption of proteoform analysis among scientists in the broader biomedical community.

抽象的 我实验室的主要重点是开发蛋白质分析新技术，特别是 围绕蛋白质组的概念。蛋白质形式，每一种都包含独特的组合 氨基酸序列和翻译后修饰（PTM）是细胞的主要分子效应器 功能。蛋白质形式之间的细微序列和 PTM 差异可以完全改变它们的功能和 活动。我们认为生物系统的全面蛋白质水平分析对于 了解它们的功能，包括细胞内运作的个体途径和网络等等 在全球范围内，破译控制细胞反应的系统生物学水平的动力学和相互作用。为了 例如，我们的项目之一是阐明特定核酸序列和 蛋白质形式与那些 DNA 或 RNA 分子结合。然而，当今的全球蛋白质组技术 复杂系统分析尚处于起步阶段，既带来了巨大的挑战，也带来了巨大的机遇。我们寻求 开发复杂系统中全面蛋白质型识别和定量的新策略。 我们设想结合来自多个数据流的信息，例如转录组数据（以揭示剪接 形式和遗传变异）、自下而上的蛋白质组学数据（揭示和定位 PTM）、自上而下的蛋白质组学 数据（为蛋白质形式识别提供序列标签）和完整质量测量（以识别和 使用来自所有其他数据流的信息来量化蛋白质形式）。具体项目将制定 以下：（1）用于构建样本特异性蛋白质组数据库的强大工具； (2)新策略 PTM 的发现和定位； (3) 改进的样品制备、分离和质谱分析 完整蛋白质的方法； (4) 利用完整质量测量和 选择自上而下的片段以最大限度地识别蛋白质形式； (5) 可视化工具 显示相关蛋白质型之间的联系和变化的蛋白质型家族。我们将整合这些 方法和数据流与强大的开源软件和随附的协议一起使 这些功能广泛可用，使世界各地的研究人员能够更深入地了解 他们的生物系统的功能。我们将把我们的创新工具应用到许多尖端项目中 许多合作者，都是因为技术开发在相关背景下最有意义 生物学研究，因为它将增加科学家们对蛋白质型分析的采用 更广泛的生物医学界。