Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang Province, 310024, China.
Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang Province, 310024, China.
Proteomics. 2020 Sep;20(17-18):e1900276. doi: 10.1002/pmic.201900276. Epub 2020 May 19.
This review provides a brief overview of the development of data-independent acquisition (DIA) mass spectrometry-based proteomics and selected DIA data analysis tools. Various DIA acquisition schemes for proteomics are summarized first including Shotgun-CID, DIA, MS , PAcIFIC, AIF, SWATH, MSX, SONAR, WiSIM, BoxCar, Scanning SWATH, diaPASEF, and PulseDIA, as well as the mass spectrometers enabling these methods. Next, the software tools for DIA data analysis are classified into three groups: library-based tools, library-free tools, and statistical validation tools. The approaches are reviewed for generating spectral libraries for six selected library-based DIA data analysis software tools which are tested by the authors, including OpenSWATH, Spectronaut, Skyline, PeakView, DIA-NN, and EncyclopeDIA. An increasing number of library-free DIA data analysis tools are developed including DIA-Umpire, Group-DIA, PECAN, PEAKS, which facilitate identification of novel proteoforms. The authors share their user experience of when to use DIA-MS, and several selected DIA data analysis software tools. Finally, the state of the art DIA mass spectrometry and software tools, and the authors' views of future directions are summarized.
这篇综述简要概述了基于数据非依赖性采集（DIA）的质谱蛋白质组学的发展以及一些选定的 DIA 数据分析工具。首先总结了各种用于蛋白质组学的 DIA 采集方案，包括 Shotgun-CID、DIA、MS、PAcIFIC、AIF、SWATH、MSX、SONAR、WiSIM、BoxCar、Scanning SWATH、diaPASEF 和 PulseDIA，以及实现这些方法的质谱仪。接下来，将 DIA 数据分析的软件工具分为三类：基于库的工具、无库工具和统计验证工具。作者对用于生成六个选定的基于库的 DIA 数据分析软件工具的光谱库的方法进行了回顾，这些工具已由作者进行了测试，包括 OpenSWATH、Spectronaut、Skyline、PeakView、DIA-NN 和 EncyclopeDIA。现在开发了越来越多的无库 DIA 数据分析工具，包括 DIA-Umpire、Group-DIA、PECAN、PEAKS，这些工具有助于鉴定新的蛋白异构体。作者分享了他们使用 DIA-MS 的用户体验，以及几个选定的 DIA 数据分析软件工具。最后，总结了 DIA 质谱和软件工具的最新进展以及作者对未来方向的看法。
