Data-Independent Acquisition Mass Spectrometry-Based Proteomics and Software Tools: A Glimpse in 2020.
Proteomics
; 20(17-18): e1900276, 2020 09.
Article
em En
| MEDLINE
| ID: mdl-32275110
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.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Proteômica
Idioma:
En
Revista:
Proteomics
Assunto da revista:
BIOQUIMICA
Ano de publicação:
2020
Tipo de documento:
Article
País de afiliação:
China