Journal of Proteomics ( IF 2.8 ) Pub Date : 2020-05-29 , DOI: 10.1016/j.jprot.2020.103844 Daniel S Ziemianowicz 1 , Vladimir Sarpe 2 , D Alex Crowder 1 , Troy J Pells 1 , Shaunak Raval 3 , Morgan Hepburn 1 , Atefeh Rafiei 3 , David C Schriemer 4
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Structural Mass Spectrometry (SMS) provides a comprehensive toolbox for the analysis of protein structure and function. It offers multiple sources of structural information that are increasingly useful for integrative structural modeling of complex protein systems. As MS-based structural workflows scale to larger systems, consistent and coherent data interpretation resources are needed to better support modeling. Unlike the proteomics community, practitioners of SMS lack adequate computational tools. Here, we review new developments in the Mass Spec Studio: an expandable ecosystem of workflows for the analysis of complementary SMS techniques with linkages to modeling. Current functionality in the Studio (version 2) supports three major SMS workflows (crosslinking, hydrogen/deuterium exchange and covalent labelling) and two pipelines for structural modeling, with a special focus on data integration. The Mass Spec Studio is an architecture focused on rapid and robust extension of functionality by a community of developers.
Significance
This review surveys the new data analysis capabilities within the Mass Spec Studio, a rich framework for rapid software development specifically targeting the community of structural proteomics and structural mass spectrometry. Updates to crosslinking, hydrogen/deuterium-exchange and covalent labeling apps are provided as well as a utility for translating such analyses into restraints that support integrative structural modeling. These new capabilities, together with the underlying design tools and content, provide the community with a wealth of resources to tackle complex structural problem and design new approaches to data analysis.
中文翻译：
在质谱工作室中协调结构质谱分析。
结构质谱（SMS）提供了用于分析蛋白质结构和功能的综合工具箱。它提供了多种结构信息来源，这些信息对于复杂蛋白质系统的集成结构建模越来越有用。随着基于MS的结构工作流程扩展到更大的系统，需要一致且一致的数据解释资源来更好地支持建模。与蛋白质组学界不同，SMS的从业者缺乏足够的计算工具。在这里，我们将回顾Mass Studio的最新发展：可扩展的工作流程生态系统，用于分析与建模相关的补充SMS技术。Studio（版本2）中的当前功能支持三种主要的SMS工作流程（交联，氢/氘交换和共价标记）和两条用于结构建模的管道，特别侧重于数据集成。Mass Spec Studio是一种体系结构，致力于由开发人员社区快速而强大地扩展功能。
意义
这篇评论调查了Mass Studio中的新数据分析功能，这是一个快速开发软件的丰富框架，专门针对结构蛋白质组学和结构质谱学领域。提供了对交联，氢/氘交换和共价标记应用程序的更新，以及用于将此类分析转换为支持集成结构建模的约束的实用程序。这些新功能以及基础设计工具和内容为社区提供了丰富的资源来解决复杂的结构问题并设计新的数据分析方法。
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