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Utilities for Annotation of Metabolomics Data

Bioconductor version: Release (3.19)

High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.

Author: Michael Witting [aut] , Johannes Rainer [aut, cre] , Andrea Vicini [aut] , Carolin Huber [aut] , Philippine Louail [aut] , Nir Shachaf [ctb]

Maintainer: Johannes Rainer <Johannes.Rainer at>

Citation (from within R, enter citation("MetaboAnnotation")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Annotation of MS-based Metabolomics Data HTML R Script
Reference Manual PDF


biocViews Infrastructure, MassSpectrometry, Metabolomics, Software
Version 1.8.1
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License Artistic-2.0
Depends R (>= 4.0.0)
Imports BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics, methods, S4Vectors, Spectra(>= 1.13.2), BiocParallel, SummarizedExperiment, QFeatures, AnnotationHub, graphics, CompoundDb
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Suggests testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny, shinyjs, DT, microbenchmark, mzR
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MetaboAnnotation_1.8.1.tar.gz
Windows Binary
macOS Binary (x86_64) MetaboAnnotation_1.8.1.tgz
macOS Binary (arm64) MetaboAnnotation_1.8.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive