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

描述（由申请人提供）：基于质谱的蛋白质组学是鉴定、定量和比较蛋白质及其翻译后修饰在生物学各个方面的关键技术。蛋白质组学工作流程的一个主要障碍是缺乏灵活和可定制的计算框架来生成数据分析软件管道。当前的软件管道通常是静态的，在创建它们的特定分析之外具有有限的灵活性，并且通常由于很少或没有维护而滞后。因此，这些工具在统计验证等领域缺乏广泛的功能和改进，限制了软件的潜力，仅通过黑匣子工具进行频谱匹配。为了解决这些障碍，在过去的12年里，我们一直在开发、维护和分发最前沿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Trans-Proteomic Pipeline。伴随着软件开发，我们通过对所有感兴趣的蛋白质组学社区用户进行广泛的辅导来确保广泛的社区采用。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认证。然而，随着新型质谱仪器的出现，现在试图提供全面的分析，必须不断维护软件工具，并在可扩展和灵活的框架中开发新功能，以确保稳健的常规操作，以便为用户社区，从新手到最极端的电源专家，提供值得信赖的结果。Trans-Proteomic Pipeline是满足这些要求的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。Trans-Proteomic Pipeline的持续开发和维护计划建立在健壮的工具开发成功方法的基础上，重点是蛋白质组学数据的“从头到尾分析”。随着“摩尔定律”水平上不断增加的数据收集率，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，如能够在单次分析中提供接近完整蛋白质组定量的多路数据独立分析，用于样品特定数据库的下一代RNA-seq基因组分析的集成，用于自信的位点特异性鉴定的翻译后修饰统计分析，以及

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.