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Rainer, J.* ; Vicini, A.* ; Salzer, L. ; Stanstrup, J.* ; Badia, J.M.* ; Neumann, S.* ; Stravs, M.A.* ; Hernandes, V.V.* ; Gatto, L.* ; Gibb, S.* ; Witting, M.

A modular and expandable ecosystem for metabolomics data annotation in R.

Metabolites 12:173 (2022)
Verlagsversion Forschungsdaten DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
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.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter Annotation ; Metabolomics ; R Programming ; Reproducible Research ; Small-compound Databases ; Untargeted Analysis
ISSN (print) / ISBN 2218-1989
e-ISSN 2218-1989
Zeitschrift Metabolites
Quellenangaben Band: 12, Heft: 2, Seiten: , Artikelnummer: 173 Supplement: ,
Verlag MDPI
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) CF Metabolomics & Proteomics (CF-MPC)
Research Unit Analytical BioGeoChemistry (BGC)
Förderungen Deutsche Forschungsgemeinschaft
University of the Autonomous Province
Bundesministerium für Bildung und Forschung
Eidgenössische Anstalt für Wasserversorgung Abwasserreinigung und Gewässerschutz