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Comparative Evaluation of Data Dependent and Data Independent Acquisition Workflows Implemented on an Orbitrap Fusion for Untargeted Metabolomics

Constant improvements to the Orbitrap mass analyzer, such as acquisition speed, resolution, dynamic range and sensitivity have strengthened its value for the large-scale identification and quantification of metabolites in complex biological matrices. Here, we report the development and optimization...

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Autores principales: Barbier Saint Hilaire, Pierre, Rousseau, Kathleen, Seyer, Alexandre, Dechaumet, Sylvain, Damont, Annelaure, Junot, Christophe, Fenaille, François
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7240956/
https://www.ncbi.nlm.nih.gov/pubmed/32325648
http://dx.doi.org/10.3390/metabo10040158
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author Barbier Saint Hilaire, Pierre
Rousseau, Kathleen
Seyer, Alexandre
Dechaumet, Sylvain
Damont, Annelaure
Junot, Christophe
Fenaille, François
author_facet Barbier Saint Hilaire, Pierre
Rousseau, Kathleen
Seyer, Alexandre
Dechaumet, Sylvain
Damont, Annelaure
Junot, Christophe
Fenaille, François
author_sort Barbier Saint Hilaire, Pierre
collection PubMed
description Constant improvements to the Orbitrap mass analyzer, such as acquisition speed, resolution, dynamic range and sensitivity have strengthened its value for the large-scale identification and quantification of metabolites in complex biological matrices. Here, we report the development and optimization of Data Dependent Acquisition (DDA) and Sequential Window Acquisition of all THeoretical fragment ions (SWATH-type) Data Independent Acquisition (DIA) workflows on a high-field Orbitrap Fusion(TM) Tribrid(TM) instrument for the robust identification and quantification of metabolites in human plasma. By using a set of 47 exogenous and 72 endogenous molecules, we compared the efficiency and complementarity of both approaches. We exploited the versatility of this mass spectrometer to collect meaningful MS/MS spectra at both high- and low-mass resolution and various low-energy collision-induced dissociation conditions under optimized DDA conditions. We also observed that complex and composite DIA-MS/MS spectra can be efficiently exploited to identify metabolites in plasma thanks to a reference tandem spectral library made from authentic standards while also providing a valuable data resource for further identification of unknown metabolites. Finally, we found that adding multi-event MS/MS acquisition did not degrade the ability to use survey MS scans from DDA and DIA workflows for the reliable absolute quantification of metabolites down to 0.05 ng/mL in human plasma.
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spelling pubmed-72409562020-06-11 Comparative Evaluation of Data Dependent and Data Independent Acquisition Workflows Implemented on an Orbitrap Fusion for Untargeted Metabolomics Barbier Saint Hilaire, Pierre Rousseau, Kathleen Seyer, Alexandre Dechaumet, Sylvain Damont, Annelaure Junot, Christophe Fenaille, François Metabolites Article Constant improvements to the Orbitrap mass analyzer, such as acquisition speed, resolution, dynamic range and sensitivity have strengthened its value for the large-scale identification and quantification of metabolites in complex biological matrices. Here, we report the development and optimization of Data Dependent Acquisition (DDA) and Sequential Window Acquisition of all THeoretical fragment ions (SWATH-type) Data Independent Acquisition (DIA) workflows on a high-field Orbitrap Fusion(TM) Tribrid(TM) instrument for the robust identification and quantification of metabolites in human plasma. By using a set of 47 exogenous and 72 endogenous molecules, we compared the efficiency and complementarity of both approaches. We exploited the versatility of this mass spectrometer to collect meaningful MS/MS spectra at both high- and low-mass resolution and various low-energy collision-induced dissociation conditions under optimized DDA conditions. We also observed that complex and composite DIA-MS/MS spectra can be efficiently exploited to identify metabolites in plasma thanks to a reference tandem spectral library made from authentic standards while also providing a valuable data resource for further identification of unknown metabolites. Finally, we found that adding multi-event MS/MS acquisition did not degrade the ability to use survey MS scans from DDA and DIA workflows for the reliable absolute quantification of metabolites down to 0.05 ng/mL in human plasma. MDPI 2020-04-18 /pmc/articles/PMC7240956/ /pubmed/32325648 http://dx.doi.org/10.3390/metabo10040158 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Barbier Saint Hilaire, Pierre
Rousseau, Kathleen
Seyer, Alexandre
Dechaumet, Sylvain
Damont, Annelaure
Junot, Christophe
Fenaille, François
Comparative Evaluation of Data Dependent and Data Independent Acquisition Workflows Implemented on an Orbitrap Fusion for Untargeted Metabolomics
title Comparative Evaluation of Data Dependent and Data Independent Acquisition Workflows Implemented on an Orbitrap Fusion for Untargeted Metabolomics
title_full Comparative Evaluation of Data Dependent and Data Independent Acquisition Workflows Implemented on an Orbitrap Fusion for Untargeted Metabolomics
title_fullStr Comparative Evaluation of Data Dependent and Data Independent Acquisition Workflows Implemented on an Orbitrap Fusion for Untargeted Metabolomics
title_full_unstemmed Comparative Evaluation of Data Dependent and Data Independent Acquisition Workflows Implemented on an Orbitrap Fusion for Untargeted Metabolomics
title_short Comparative Evaluation of Data Dependent and Data Independent Acquisition Workflows Implemented on an Orbitrap Fusion for Untargeted Metabolomics
title_sort comparative evaluation of data dependent and data independent acquisition workflows implemented on an orbitrap fusion for untargeted metabolomics
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7240956/
https://www.ncbi.nlm.nih.gov/pubmed/32325648
http://dx.doi.org/10.3390/metabo10040158
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