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Review
. 2020 Sep;20(17-18):e1900276.
doi: 10.1002/pmic.201900276. Epub 2020 May 19.

Data-Independent Acquisition Mass Spectrometry-Based Proteomics and Software Tools: A Glimpse in 2020

Fangfei Zhang  1   2 , Weigang Ge  1   2 , Guan Ruan  1   2 , Xue Cai  1   2 , Tiannan Guo  1   2
Affiliations
Review

Data-Independent Acquisition Mass Spectrometry-Based Proteomics and Software Tools: A Glimpse in 2020

Fangfei Zhang et al. Proteomics. 2020 Sep.

Abstract

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, MSE , 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.

Keywords: data-independent acquisition; database search; software tools; spectral library; targeted proteomics.

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