Fangfei Zhang et al, Data-Independent Acquisition Mass Spectrometry-based Proteomics and Software Tools: A Glimpse in 2020, 10 April 2020, https://doi.org/10.1002/pmic.201900276
This review provides a brief overview of the development of data‐independent acquisition (DIA) mass spectrometry‐based proteomics and selected DIA data analysis tools. We first summarize various DIA acquisition schemes for proteomics 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, we categorize the software tools for DIA data analysis into three groups: library‐based tools, library‐free tools and statistical validation tools. We review the approaches for generating spectral libraries for six selected library‐based DIA data analysis software tools which have been tested by the authors, including OpenSWATH, Spectronaut, Skyline, PeakView, DIA‐NN and EncyclopeDIA. An increasing number of library‐free DIA data analysis tools have been developed including DIA‐Umpire, Group‐DIA, PECAN, PEAKS, which facilitate identification of novel proteoforms. We share our user experience of when to use DIA‐MS, and several selected DIA data analysis software tools. Finally, we summarize the state of the art of DIA mass spectrometry and software tools, and our views of future directions.