Development of Trans Proteomic Pipeline, an Analysis Suite for Mass Spectrometry

开发反式蛋白质组管道（质谱分析套件）

• 批准号: 8698152
• 负责人: Eric Deutsch
• 金额: $ 52.13万
• 依托单位: INSTITUTE FOR SYSTEMS BIOLOGY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-01 至 2018-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8698152
• 关键词: Address; Adoption; Algorithms; Area; Biochemistry; Biological; Biological Markers; Biology; Boxing; Cells; Clinical; Cloud Computing; Communities; Complement; Computer software; Data; Data Analyses; Data Collection; Data Set; Databases; Development; Diagnostic Procedure; Discipline; Disease; Educational process of instructing; Emerging Technologies; Ensure; Environment; Feedback; Genomics; Goals; Grant; Human; Imagery; Investigation; Laws; Linux; Maintenance; Mass Spectrum Analysis; Measurement; Monitor; Nature; Output; Post-Translational Protein Processing; Process; Production; Program Development; Proteins; Proteome; Proteomics; Protocols documentation; Reaction; Reporting; Research; Resolution; Sampling; Sensitivity and Specificity; Site; Software Tools; Speed; Staging; Stress; Students; System; Technology; Therapeutic; Tissues; Trust; Update; Validation; Western Blotting; Writing; base; complex biological systems; computer framework; computerized data processing; computerized tools; data sharing; flexibility; graphical user interface; human disease; improved; instrumentation; interest; mass spectrometer; new technology; next generation; open source; operation; programs; protein expression; public health relevance; software development; tandem mass spectrometry; technique development; tool; tool development; transcriptome sequencing

DESCRIPTION (provided by applicant): Mass spectrometry based proteomics is a key technology for the identification, quantification and comparison of proteins and their post-translational modifications across all aspects of biology. One major barrier in proteomics workflows is the paucity of flexible and customizable computational frameworks for generating data analysis software pipelines. Current software pipelines are often static, with limited flexibility beyond the specific analyses for which they were created and generally lag behind due to little or no maintenance. These tools therefore lack broad functionality and improvements in areas such as statistical validation, limiting the potential of the software to mere spectrum matching through black box tools. To address these barriers, we have been developing, maintaining and distributing cutting edge proteomics computational tools and standards in data analysis over the last 12 years through our program suite called the Trans-Proteomic Pipeline. Concomitant with software development, we ensure wide community adoption through extensive tutoring to all interested users of the proteomics community. Through our development, we have provided new functionality for proteomics data analyses with both new and improved statistical validation and global qualification. However, with new styles of mass spectrometry instrumentation that attempt to now provide comprehensive analysis, software tools must be continually maintained and new functionality developed in an extensible and flexible framework that ensures robust, routine operation so that it provides the user community, from novice to the most extreme power experts, with trusted results. The Trans-Proteomic Pipeline has been the first and most continually developed and maintained product for these requirements. Our goal of providing all these tools as both full open source and freely available complement of programs, ensures wide adoption and permits community input into the tools development for the broadest and most needed functionality possible. This continuing program of development and maintenance of the Trans-Proteomic Pipeline builds on the successful approach of robust tools development with the focus of "from start to the end analysis" of proteomics data. With ever increasing data collection rates at a "Moore's Law" level, this program will continue to develop tools to analyze these larger and larger datasets. We will develop and integrate tools for new styles of proteomic data collection such as multiplexed data-independent analysis capable of providing near full proteome quantitation in a single analysis, integration of next generation RNA-seq genomic analysis for sample specific databases, post-translational modification statistical analysis for confident site specific identification, and the implementation of new selected-reaction monitoring capabilities that drive proteomics as the next generation "Western Blot". All these efforts are underpinned by a strong computational and biochemistry focused background to ensure the tools are well written with maximum relevance to biology.

描述（由申请人提供）：基于质谱的蛋白质组学是在生物学的各个方面对蛋白质及其翻译后修饰进行鉴定、定量和比较的关键技术。蛋白质组学工作流程中的一个主要障碍是缺乏用于生成数据分析软件管道的灵活和可定制的计算框架。当前的软件管道通常是静态的，除了特定的分析之外，灵活性有限，并且由于很少或根本没有维护，通常会滞后。因此，这些工具在统计验证等领域缺乏广泛的功能和改进，将软件的潜力限制在仅仅通过黑盒工具进行光谱匹配。为了解决这些障碍，在过去的12年里，我们一直在开发，维护和分发尖端的蛋白质组学计算工具和数据分析标准，通过我们的程序套件称为跨蛋白质组学管道。伴随着软件开发，我们通过对蛋白质组学社区所有感兴趣的用户进行广泛的辅导，确保社区的广泛采用。通过我们的开发，我们为蛋白质组学数据分析提供了新的功能，包括新的和改进的统计验证和全球资格。然而，随着新型质谱仪现在试图提供全面的分析，软件工具必须不断维护，新的功能必须在可扩展和灵活的框架中开发，以确保强大的常规操作，以便为用户社区，从新手到最极端的电力专家，提供值得信赖的结果。Trans-Proteomic Pipeline是第一个也是最持续开发和维护的产品。我们的目标是提供所有这些工具作为完全开源和免费提供的程序补充，确保广泛采用，并允许社区投入到工具开发中，以实现最广泛和最需要的功能。这种持续的跨蛋白质组学管道开发和维护计划建立在强大的工具开发的成功方法之上，重点是蛋白质组学数据的“从开始到结束分析”。随着数据收集率在“摩尔定律”水平上不断提高，该计划将继续开发工具来分析这些越来越大的数据集。我们将开发和整合用于新型蛋白质组学数据收集的工具，例如能够在单一分析中提供接近完整蛋白质组定量的多路复用数据独立分析，整合下一代RNA-seq基因组分析用于样品特定数据库，翻译后修饰统计分析用于可靠的位点特异性鉴定，以及 实施新的选择性反应监测功能，推动蛋白质组学成为下一代“Western Blot”。所有这些努力都得到了强大的计算和生物化学背景的支持，以确保工具编写得很好，与生物学具有最大的相关性。