Articles producció científica> Enginyeria Electrònica, Elèctrica i Automàtica

A Modular and Expandable Ecosystem for Metabolomics Data Annotation in R

  • Identification data

    Identifier: imarina:9245943
    Authors:
    Rainer JVicini ASalzer LStanstrup JBadia JMNeumann SStravs MAHernandes VVGatto LGibb SWitting M
    Abstract:
    Liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics experiments have become increasingly popular because of the wide range of metabolites that can be analyzed and the possibility to measure novel compounds. LC-MS instrumentation and analysis conditions can differ substantially among laboratories and experiments, thus resulting in non-standardized datasets demanding customized annotation workflows. We present an ecosystem of R packages, centered around the MetaboCoreUtils, MetaboAnnotation and CompoundDb packages that together provide a modular infrastructure for the annotation of untargeted metabolomics data. Initial annotation can be performed based on MS1 properties such as m/z and retention times, followed by an MS2-based annotation in which experimental fragment spectra are compared against a reference library. Such reference databases can be created and managed with the CompoundDb package. The ecosystem supports data from a variety of formats, including, but not limited to, MSP, MGF, mzML, mzXML, netCDF as well as MassBank text files and SQL databases. Through its highly customizable functionality, the presented infrastructure allows to build reproducible annotation workflows tailored for and adapted to most untargeted LC-MS-based datasets. All core functionality, which supports base R data types, is exported, also facilitating its re-use in other R packages. Finally, all packages are thoroughly unit-tested and documented and are available on GitHub and through Bioconductor.
  • Others:

    Author, as appears in the article.: Rainer J; Vicini A; Salzer L; Stanstrup J; Badia JM; Neumann S; Stravs MA; Hernandes VV; Gatto L; Gibb S; Witting M
    Department: Enginyeria Electrònica, Elèctrica i Automàtica
    URV's Author/s: Badia Aparicio, José María
    Keywords: Untargeted analysis Tandem mass-spectra Small-compound databases Reproducible research R programming Metabolomics Annotation untargeted analysis tool small-compound databases search reproducible research r programming fragmentation annotation
    Abstract: Liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics experiments have become increasingly popular because of the wide range of metabolites that can be analyzed and the possibility to measure novel compounds. LC-MS instrumentation and analysis conditions can differ substantially among laboratories and experiments, thus resulting in non-standardized datasets demanding customized annotation workflows. We present an ecosystem of R packages, centered around the MetaboCoreUtils, MetaboAnnotation and CompoundDb packages that together provide a modular infrastructure for the annotation of untargeted metabolomics data. Initial annotation can be performed based on MS1 properties such as m/z and retention times, followed by an MS2-based annotation in which experimental fragment spectra are compared against a reference library. Such reference databases can be created and managed with the CompoundDb package. The ecosystem supports data from a variety of formats, including, but not limited to, MSP, MGF, mzML, mzXML, netCDF as well as MassBank text files and SQL databases. Through its highly customizable functionality, the presented infrastructure allows to build reproducible annotation workflows tailored for and adapted to most untargeted LC-MS-based datasets. All core functionality, which supports base R data types, is exported, also facilitating its re-use in other R packages. Finally, all packages are thoroughly unit-tested and documented and are available on GitHub and through Bioconductor.
    Thematic Areas: Molecular biology Medicina ii Farmacia Endocrinology, diabetes and metabolism Ciências biológicas ii Ciências biológicas i Biotecnología Biochemistry & molecular biology Biochemistry
    licence for use: https://creativecommons.org/licenses/by/3.0/es/
    Author's mail: josepmaria.badia@urv.cat josepmaria.badia@urv.cat josepmaria.badia@urv.cat
    Record's date: 2024-09-07
    Papper version: info:eu-repo/semantics/publishedVersion
    Link to the original source: https://www.mdpi.com/2218-1989/12/2/173
    Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
    Papper original source: Metabolites. 12 (2):
    APA: Rainer J; Vicini A; Salzer L; Stanstrup J; Badia JM; Neumann S; Stravs MA; Hernandes VV; Gatto L; Gibb S; Witting M (2022). A Modular and Expandable Ecosystem for Metabolomics Data Annotation in R. Metabolites, 12(2), -. DOI: 10.3390/metabo12020173
    Article's DOI: 10.3390/metabo12020173
    Entity: Universitat Rovira i Virgili
    Journal publication year: 2022
    Publication Type: Journal Publications
  • Keywords:

    Biochemistry,Biochemistry & Molecular Biology,Endocrinology, Diabetes and Metabolism,Molecular Biology
    Untargeted analysis
    Tandem mass-spectra
    Small-compound databases
    Reproducible research
    R programming
    Metabolomics
    Annotation
    untargeted analysis
    tool
    small-compound databases
    search
    reproducible research
    r programming
    fragmentation
    annotation
    Molecular biology
    Medicina ii
    Farmacia
    Endocrinology, diabetes and metabolism
    Ciências biológicas ii
    Ciências biológicas i
    Biotecnología
    Biochemistry & molecular biology
    Biochemistry
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