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Revealing Proteoforms: The Primary Effectors of Biological Function

揭示蛋白质形式：生物功能的主要效应器

基本信息

批准号：
10621058
负责人：
LLOYD M SMITH
金额：
$ 70.62万
依托单位：
UNIVERSITY OF WISCONSIN-MADISON
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-05-01 至 2028-08-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10621058
关键词：
Acceleration Algorithms Amino Acid Sequence Atlases Bioinformatics Biological Biological Process Biology Cell physiology Cells Complex Complex Mixtures Computer software Data Data Analyses Databases Development Dimensions Disease Dissociation Effector Cell Enzymes Genome Human Individual Intelligence Ions Laboratories Manuals Measurement Methods Molecular Pathway interactions Post Translational Modification Analysis Post-Translational Protein Processing Process Proteomics Quantitative Trait Loci Research Research Personnel Resolution Sampling Scientist Source System Systems Biology Technology Time Validation Visualization software Work biological systems complex biological systems data acquisition field study human disease infancy informatics tool interest macromolecule model organism novel strategies response tool transcriptome sequencing

项目摘要

ABSTRACT The primary focus of my laboratory is the development of new tools and strategies for proteomic analyses of complex biological systems, 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. The current technology for global proteoform analysis in complex systems is in its infancy, offering both a great challenge and a great opportunity. Our laboratory is keenly interested in tackling this problem and is pioneering a new approach that integrates high resolution proteoform intact mass measurements, both bottom-up and top-down strategies, new informatic tools for the comprehensive analysis of PTMs, and RNA-Seq information; all woven together in a robust bioinformatic framework to allow the comprehensive identification and quantification of proteoforms in complex mixtures. Along with other world-class scientists, we will work towards embarking on the Human Proteoform Project, which includes ambitious subprojects describing the construction and utility of comprehensive proteoform atlases for humans and model organisms. Specific projects in our laboratory will include development of the following: (1) a multi-dimensional separation strategy for increased breadth and depth of proteoform identifications; (2) a source-induced dissociation method for fragmentation of eluting proteoform ions to increase proteoform identifications; (3) intelligent real-time data acquisition; (4) direct acquisition of orbitrap time-domain transients to expand the accessible mass range; (5) data analysis software including the abilities to search for truncated proteoforms and utilize the most abundant mass for identification; (6) sample-specific databases created through integration of bottom-up, top-down, intact mass and RNA-Seq data; (7) visualization tools for manual validation of proteoform identifications and for troubleshooting problems with samples and/or algorithms; and (8) using proteoform quantitative trait loci (QTLs) to reveal the modifying enzymes encoded elsewhere in the genome that are responsible for the critical post-translational modifications with functional consequence. We are excited to develop powerful new tools to advance the state-of-the-art in this new and important field of study to reveal the biologically important effectors of cellular mechanisms. These tools, which will be made widely available to all researchers, will reveal new information essential to the understanding of both normal and disease biology, deepening and accelerating the study of human disease processes.

摘要我的实验室的主要重点是开发新的工具和策略，用于蛋白质组学分析，复杂的生物系统，特别是围绕蛋白形式的概念。蛋白形式，每种其包含氨基酸序列和翻译后修饰（PTM）的独特组合，是细胞功能的主要分子效应器。微妙的序列和PTM之间的差异 Proteoforms可以完全改变它们的功能和活性。我们看到全面的蛋白质水平分析生物系统对于理解它们的功能是绝对必要的，对于个体途径和网络在细胞内运作，更全球化，以破译系统生物学水平的动态，控制细胞反应的相互作用。复杂环境中蛋白质组分析的现有技术系统正处于起步阶段，既带来了巨大的挑战，也带来了巨大的机遇。我们的实验室敏锐地有兴趣解决这个问题，并正在开创一种新的方法，完整的质量测量，自下而上和自上而下的战略， PTM和RNA-Seq信息的综合分析;所有这些都编织在一个强大的生物信息学该框架允许对复杂混合物中的蛋白形式进行全面鉴定和定量。沿着其他世界级的科学家，我们将致力于人类蛋白质工程，其中包括雄心勃勃的子项目，描述了综合蛋白质的建设和效用，人类和模式生物的地图集。我们实验室的具体项目将包括开发以下：（1）多维分离策略，以增加蛋白质型的广度和深度鉴定;（2）源诱导解离法，用于洗脱蛋白形式离子的碎片化，增加蛋白质型鉴定;（3）智能实时数据采集;（4）轨道阱直接采集时域瞬态，以扩大可访问的质量范围;（5）数据分析软件，包括能力寻找截短的蛋白质型，并利用最丰富的质量进行鉴定;（6）样品特异性通过整合自下而上、自上而下、完整的质量和RNA-Seq数据创建的数据库;（7）可视化工具，用于手动验证Proteoform识别和故障排除问题样品和/或算法;和（8）使用蛋白质型数量性状基因座（QTL）来揭示修饰的基因座，在基因组的其他地方编码的酶，负责关键的翻译后修饰功能性后果。我们很高兴能够开发强大的新工具，以推动最先进的这是一个新的重要研究领域，旨在揭示细胞机制的生物学重要效应子。这些工具将广泛提供给所有研究人员，将揭示对研究至关重要的新信息。了解正常和疾病生物学，深化和加速人类疾病的研究流程.