Articles producció científica> Enginyeria Electrònica, Elèctrica i Automàtica

HERMES: a molecular-formula-oriented method to target the metabolome

  • Identification data

    Identifier: imarina:9231652
    Authors:
    Gine, RogerCapeHades, JordiBadia, Josep MVughs, DennisSchwaiger-Haber, MichaelaAlexandrov, TheodoreVinaixa, MariaBrunner, Andrea MPatti, Gary JYanes, Oscar
    Abstract:
    Comprehensive metabolome analyses are essential for biomedical, environmental, and biotechnological research. However, current MS1- and MS2-based acquisition and data analysis strategies in untargeted metabolomics result in low identification rates of metabolites. Here we present HERMES, a molecular-formula-oriented and peak-detection-free method that uses raw LC/MS1 information to optimize MS2 acquisition. Investigating environmental water, Escherichia coli, and human plasma extracts with HERMES, we achieved an increased biological specificity of MS2 scans, leading to improved mass spectral similarity scoring and identification rates when compared with a state-of-the-art data-dependent acquisition (DDA) approach. Thus, HERMES improves sensitivity, selectivity, and annotation of metabolites. HERMES is available as an R package with a user-friendly graphical interface for data analysis and visualization.HERMES is a molecular-formula-oriented and peak-detection-free method that uses LC/MS1 information to optimize MS2 acquisition for LC/MS-based metabolomic analysis.
  • Others:

    Author, as appears in the article.: Gine, Roger; CapeHades, Jordi; Badia, Josep M; Vughs, Dennis; Schwaiger-Haber, Michaela; Alexandrov, Theodore; Vinaixa, Maria; Brunner, Andrea M; Patti, Gary J; Yanes, Oscar
    Department: Enginyeria Electrònica, Elèctrica i Automàtica
    URV's Author/s: Giné Bertomeu, Roger / Vinaixa Crevillent, Maria / Yanes Torrado, Óscar
    Keywords: Xcms Water pollutants, chemical Tandem mass spectrometry Platform Plasma Metabolomics Metabolome Mass-spectrometry data Humans Features Escherichia coli Database Chromatography, liquid Annotation Algorithms
    Abstract: Comprehensive metabolome analyses are essential for biomedical, environmental, and biotechnological research. However, current MS1- and MS2-based acquisition and data analysis strategies in untargeted metabolomics result in low identification rates of metabolites. Here we present HERMES, a molecular-formula-oriented and peak-detection-free method that uses raw LC/MS1 information to optimize MS2 acquisition. Investigating environmental water, Escherichia coli, and human plasma extracts with HERMES, we achieved an increased biological specificity of MS2 scans, leading to improved mass spectral similarity scoring and identification rates when compared with a state-of-the-art data-dependent acquisition (DDA) approach. Thus, HERMES improves sensitivity, selectivity, and annotation of metabolites. HERMES is available as an R package with a user-friendly graphical interface for data analysis and visualization.HERMES is a molecular-formula-oriented and peak-detection-free method that uses LC/MS1 information to optimize MS2 acquisition for LC/MS-based metabolomic analysis.
    Thematic Areas: Molecular biology Interdisciplinar General medicine Engenharias iv Ciências biológicas ii Ciências biológicas i Cell biology Biotechnology Biochemistry Biochemical research methods
    licence for use: https://creativecommons.org/licenses/by/3.0/es/
    Author's mail: roger.gine@urv.cat maria.vinaixa@urv.cat oscar.yanes@urv.cat maria.vinaixa@urv.cat
    Author identifier: 0000-0001-9804-0171 0000-0003-3695-7157 0000-0001-9804-0171
    Record's date: 2024-10-12
    Papper version: info:eu-repo/semantics/acceptedVersion
    Link to the original source: https://www.nature.com/articles/s41592-021-01307-z
    Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
    Papper original source: Nature Methods. 18 (11): 1370-+
    APA: Gine, Roger; CapeHades, Jordi; Badia, Josep M; Vughs, Dennis; Schwaiger-Haber, Michaela; Alexandrov, Theodore; Vinaixa, Maria; Brunner, Andrea M; Patt (2021). HERMES: a molecular-formula-oriented method to target the metabolome. Nature Methods, 18(11), 1370-+. DOI: 10.1038/s41592-021-01307-z
    Article's DOI: 10.1038/s41592-021-01307-z
    Entity: Universitat Rovira i Virgili
    Journal publication year: 2021
    Publication Type: Journal Publications
  • Keywords:

    Biochemical Research Methods,Biochemistry,Biotechnology,Cell Biology,Molecular Biology
    Xcms
    Water pollutants, chemical
    Tandem mass spectrometry
    Platform
    Plasma
    Metabolomics
    Metabolome
    Mass-spectrometry data
    Humans
    Features
    Escherichia coli
    Database
    Chromatography, liquid
    Annotation
    Algorithms
    Molecular biology
    Interdisciplinar
    General medicine
    Engenharias iv
    Ciências biológicas ii
    Ciências biológicas i
    Cell biology
    Biotechnology
    Biochemistry
    Biochemical research methods
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