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Data-Independent Acquisition Mass Spectrometry-Based Proteomics and Software Tools: A Glimpse in 2020
Fangfei Zhang1,2, Weigang Ge1,2, Guan Ruan1,2
1Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang Province, 310024, China.
Proteomics
|April 11, 2020
Summary
This review covers data-independent acquisition (DIA) mass spectrometry for proteomics and its analysis tools. It summarizes DIA methods and software, aiding researchers in selecting appropriate techniques for proteomic studies.
Area of Science:
- Proteomics
- Mass Spectrometry
- Biotechnology
Background:
- Data-independent acquisition (DIA) mass spectrometry has advanced proteomics.
- Various DIA acquisition schemes and enabling mass spectrometers exist.
- Efficient data analysis is crucial for DIA proteomics.
Purpose of the Study:
- To review the development of DIA mass spectrometry in proteomics.
- To summarize and classify DIA data analysis software tools.
- To provide user experience and future directions for DIA proteomics.
Main Methods:
- Summarized various DIA acquisition schemes (e.g., SWATH, diaPASEF).
- Classified DIA data analysis tools into library-based, library-free, and validation categories.
- Reviewed spectral library generation and tested selected software (OpenSWATH, Spectronaut, Skyline, PeakView, DIA-NN, EncyclopeDIA).
Main Results:
- Detailed various DIA methods and mass spectrometers.
- Highlighted library-based tools and library-free tools (e.g., DIA-Umpire, PEAKS) for novel proteoform identification.
- Shared user experience on selecting DIA-MS and software.
Conclusions:
- DIA mass spectrometry offers powerful proteomic analysis capabilities.
- A range of software tools are available for DIA data analysis, with ongoing development.
- Future directions include advancements in DIA technology and analytical software.