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A modular and expandable ecosystem for metabolomics data annotation in R.
Metabolites 12:173 (2022)
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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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Annotation ; Metabolomics ; R Programming ; Reproducible Research ; Small-compound Databases ; Untargeted Analysis
ISSN (print) / ISBN
2218-1989
e-ISSN
2218-1989
Journal
Metabolites
Quellenangaben
Volume: 12,
Issue: 2,
Article Number: 173
Publisher
MDPI
Non-patent literature
Publications
Reviewing status
Peer reviewed
Grants
Deutsche Forschungsgemeinschaft
University of the Autonomous Province
Bundesministerium für Bildung und Forschung
Eidgenössische Anstalt für Wasserversorgung Abwasserreinigung und Gewässerschutz
University of the Autonomous Province
Bundesministerium für Bildung und Forschung
Eidgenössische Anstalt für Wasserversorgung Abwasserreinigung und Gewässerschutz