MASH Explorer, a Comprehensive Software Environment for Top-Down Proteomics

MASH Explorer，自上而下蛋白质组学的综合软件环境

• 批准号: 9904714
• 负责人: Ying Ge
• 金额: $ 28.94万
• 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: 2018-06-01 至 2022-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9904714
• 关键词: Academia; Address; Algorithms; Alternative Splicing; Attention; Biomedical Research; Cell physiology; Collaborations; Communities; Complex; Computer software; Data; Data Analyses; Data Files; Data Storage and Retrieval; Databases; Development; Disease; Environment; Family; Genetic Variation; Genome; Genomics; Goals; Growth; Industrialization; Industry; Mass Spectrum Analysis; Methods; Online Systems; Pathway interactions; Play; Post-Translational Protein Processing; Process; Proteins; Proteome; Proteomics; Research Personnel; Resolution; Role; Software Tools; System; Time; Vendor; amyloid precursor protein processing; automated algorithm; base; cloud based; cluster computing; computerized data processing; cost; data and analysis portal; data sharing; data warehouse; design; frontier; graphical user interface; human disease; improved; innovation; instrument; instrumentation; interest; mass spectrometer; new therapeutic target; novel; personalized medicine; rapid growth; software development; therapeutic protein; tool; ultra high resolution; user friendly software; user-friendly

Project Summary In the post-genomic era, proteomics is the next frontier allowing an in-depth understanding of the function of cellular systems in human diseases and the development of personalized treatments. Unlike the genome, the proteome is dynamic and highly complex due to alternative splicing and post-translational modifications (PTMs). The emerging top-down proteomics is the most powerful method to comprehensively characterize proteoforms that arise from genetic variations and PTMs, which is critical for understanding disease mechanisms and identifying new therapeutic targets. However, data analysis tools for top-down proteomics remain under- developed. With the recent rapid growth of the top-down proteomics community, there is an urgent need to develop a comprehensive analysis platform for top-down proteomics. Herein, we aim to develop MASH Explorer, a comprehensive, universal, and user-friendly software environment for top-down proteomics, which includes both an offline downloadable software package (App) and an online version for data processing and analysis (Portal). The specific aims are: 1) to develop MASH Explorer App, a downloadable software package for top- down proteomics that can process data from various vendor formats and incorporate multiple algorithms for deconvolution and database search with user-friendly graphical interfaces; a novel deconvolution algorithm for high-accuracy data analysis and a novel search algorithm for identification of large proteins will also be developed to address the deficiency in the currently available top-down proteomcis software tools; 2) to develop novel algorithms for the automated identification and quantification of proteoform families with enhanced identification of low-abundance proteoforms; 3) to develop MASH Explorer Portal, a web-based extension of MASH Explorer App for processing and sharing top-down proteomics data. The MASH Explorer Portal features my MASH, a cloud-based personalized space for online data processing, as well as MASH public, a public database for long-term data storage and sharing to facilitate the collaboration among various groups and the entire proteomics community. The successful completion of this project will create a powerful software tool, MASH Explorer, for top-down proteomics. The MASH Explorer software will be freely available to all users. Improving the accessibility of non-proprietary free software solutions will significantly bolster the growth of the top-down proteomics community. Hence, we envision it will play integral roles in advancing the burgeoning field of top-down proteomics and realize its full potential for biomedical research.

项目概要 在后基因组时代，蛋白质组学是深入了解功能的下一个前沿领域 人类疾病中的细胞系统和个性化治疗的开发。与基因组不同的是， 由于选择性剪接和翻译后修饰 (PTM)，蛋白质组是动态且高度复杂的。 新兴的自上而下的蛋白质组学是全面表征蛋白质形式的最有力的方法 由遗传变异和 PTM 产生，这对于理解疾病机制和 确定新的治疗靶点。然而，自上而下的蛋白质组学数据分析工具仍然不足 发达。随着自上而下蛋白质组学界最近的快速发展，迫切需要 开发自上而下的蛋白质组学综合分析平台。在此，我们的目标是开发 MASH Explorer， 一个全面、通用且用户友好的自上而下蛋白质组学软件环境，其中包括 既有离线下载的软件包（App），也有用于数据处理和分析的在线版本 （门户网站）。具体目标是：1）开发MASH Explorer App，这是一个可下载的软件包，用于顶级- 蛋白质组学可以处理来自各种供应商格式的数据并结合多种算法 通过用户友好的图形界面进行反卷积和数据库搜索；一种新颖的反卷积算法 高精度数据分析和用于识别大蛋白质的新颖搜索算法也将 旨在解决当前可用的自上而下的蛋白质组学软件工具的缺陷； 2）开发 用于自动识别和量化蛋白质家族的新算法，具有增强的 低丰度蛋白型的鉴定； 3) 开发 MASH Explorer Portal，一个基于 Web 的扩展 MASH Explorer 应用程序用于处理和共享自上而下的蛋白质组数据。 MASH Explorer 门户功能 my MASH，一个基于云的个性化在线数据处理空间，以及 MASH public，一个公共空间 数据库用于长期数据存储和共享，以促进各个群体和组织之间的协作 整个蛋白质组学界。该项目的成功完成将创建一个强大的软件工具， MASH Explorer，用于自上而下的蛋白质组学。 MASH Explorer 软件将免费提供给所有用户。 提高非专有自由软件解决方案的可访问性将显着促进非专有自由软件解决方案的增长 自上而下的蛋白质组学社区。因此，我们预计它将在推动这一新兴领域发挥不可或缺的作用 自上而下的蛋白质组学并充分发挥其在生物医学研究方面的潜力。