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^E, 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.

中文翻译：

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基于数据独立采集质谱的蛋白质组学和软件工具：2020 年的一瞥。

本综述简要概述了基于数据独立采集 (DIA) 质谱的蛋白质组学和选定的 DIA 数据分析工具的发展。首先总结了蛋白质组学的各种 DIA 采集方案，包括 Shotgun-CID、DIA、MS ^E、PAcIFIC、AIF、SWATH、MSX、SONAR、WiSIM、BoxCar、Scanning SWATH、diaPASEF 和 PulseDIA，以及支持这些方法的质谱仪。接下来，用于 DIA 数据分析的软件工具分为三组：基于库的工具、无库的工具和统计验证工具。审查了为六种选定的基于库的 DIA 数据分析软件工具生成光谱库的方法，这些工具由作者测试，包括 OpenSWATH、Spectronaut、Skyline、PeakView、DIA-NN 和 EncyclopeDIA。越来越多的无库 DIA 数据分析工具被开发出来，包括 DIA-Umpire、Group-DIA、PECAN、PEAKS，这些工具有助于识别新的蛋白质型。作者分享了他们何时使用 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，