Data acquisition workflows in liquid chromatography coupled to high resolution mass spectrometry-based metabolomics: Where do we stand?

Journal of Chromatography. a
François FenailleChristophe Junot

Abstract

Typical mass spectrometry (MS) based untargeted metabolomics protocols are tedious as well as time- and sample-consuming. In particular, they often rely on "full-scan-only" analyses using liquid chromatography (LC) coupled to high resolution mass spectrometry (HRMS) from which metabolites of interest are first highlighted, and then tentatively identified by using targeted MS/MS experiments. However, this situation is evolving with the emergence of integrated HRMS based-data acquisition protocols able to perform multi-event acquisitions. Most of these protocols, referring to as data dependent and data independent acquisition (DDA and DIA, respectively), have been initially developed for proteomic applications and have recently demonstrated their applicability to biomedical studies. In this context, the aim of this article is to take stock of the progress made in the field of DDA- and DIA-based protocols, and evaluate their ability to change conventional metabolomic and lipidomic data acquisition workflows, through a review of HRMS instrumentation, DDA and DIA workflows, and also associated informatics tools.

Citations

Jul 20, 2019·Proteomics·Danielle L PetersDaniel Figeys
Dec 11, 2019·Analytical and Bioanalytical Chemistry·Thomas ZülligHarald C Köfeler
Jun 25, 2020·Proteomics·Sanjeev DahalLaurence Yang
Apr 2, 2020·Mass Spectrometry Reviews·Thomas Züllig, Harald C Köfeler
Jan 20, 2020·Metabolomics : Official Journal of the Metabolomic Society·Graciela CarlosPedro Eduardo Fröehlich
Jan 22, 2020·Scientific Reports·Elena GorokhovaHitesh V Motwani
Sep 22, 2020·Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics·David A DreierChristopher J Martyniuk
Jun 20, 2021·Mass Spectrometry Reviews·Emmanuel DefossezGaétan Glauser
Aug 11, 2021·Analytical Chemistry·Premy ShanthamoorthyHannes Röst
Aug 26, 2021·Analytical and Bioanalytical Chemistry·Florence Anne CastelliChristophe Junot
Nov 18, 2021·The Analyst·Takayuki KawaiKoji Otsuka
Dec 21, 2021·Frontiers in Plant Science·Lisa S MydyRoland D Kersten

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