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.

抽象的我实验室的主要重点是开发新工具和策略，以进行蛋白质组学分析复杂的生物系统，特别围绕蛋白质类型的概念为中心。蛋白质成型，每个它包括氨基酸序列和翻译后修饰（PTMS）的独特组合，是细胞功能的主要分子效应子。微妙的序列和PTM差异蛋白质类型可以完全改变其功能和活性。我们看到全面的蛋白质级分析生物系统对于理解其功能，个人途径和网络在细胞内以及更全球范围内操作，以破译系统生态级动力学和控制细胞反应的相互作用。复杂的全球蛋白质分析的当前技术系统还处于起步阶段，既带来了巨大的挑战，也是一个巨大的机会。我们的实验室敏锐有兴趣解决这个问题，并开创了一种集成高分辨率蛋白质成型的新方法完整的质量测量，自下而上和自上而下的策略，新的信息工具 PTM和RNA-Seq信息的全面分析；所有这些都在强大的生物信息中编织在一起框架以允许在复杂混合物中综合鉴定和量化蛋白质成型。与其他世界一流的科学家一起，我们将致力于着手进行人类蛋白质成型项目，其中包括描述综合蛋白质成型的构建和实用性的雄心勃勃的副标题人类和模型生物的地图集。我们实验室中的特定项目将包括开发如下：（1）一种多维分离策略，以增加蛋白质成型的宽度和深度识别；（2）一种源诱导的解离法，用于将蛋白质成型离子碎裂至增加蛋白质型鉴定；（3）智能实时数据获取；（4）直接获取Orbitrap 时间域瞬变以扩大可访问质量范围；（5）包括能力在内的数据分析软件搜索截短的蛋白质成型，并利用最丰富的质量来识别；（6）特定于样本通过整合自下而上，自上而下，完整质量和RNA-seq数据而创建的数据库；（7）可视化工具，用于手动验证蛋白质成型识别以及解决问题的问题样品和/或算法；（8）使用蛋白质成型定量性状基因座（QTL）揭示了修饰基因组其他地方编码的酶负责关键的翻译后修饰具有功能后果。我们很高兴开发强大的新工具来推进最先进的工具这一新的重要研究领域揭示了细胞机制的生物学重要效应因子。这些工具将被广泛提供给所有研究人员，将揭示对该工具的新信息了解正常和疾病生物学，加深和加速人类疾病过程。