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Creating and Using (Chemical) Compound Annotation Databases

Bioconductor version: Release (3.19)

CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor's Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.

Author: Jan Stanstrup [aut] , Johannes Rainer [aut, cre] , Josep M. Badia [ctb] , Roger Gine [aut] , Andrea Vicini [aut]

Maintainer: Johannes Rainer <johannes.rainer at>

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


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:

Creating CompoundDb annotation resources HTML R Script
Usage of Annotation Resources with the CompoundDb Package HTML R Script
Reference Manual PDF


biocViews Annotation, MassSpectrometry, Metabolomics, Software
Version 1.8.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License Artistic-2.0
Depends R (>= 4.1), methods, AnnotationFilter, S4Vectors
Imports BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr, RSQLite, Biobase, ProtGenerics(>= 1.35.3), xml2, IRanges, Spectra(>= 1.9.12), MsCoreUtils, MetaboCoreUtils, BiocParallel
System Requirements
Bug Reports
See More
Suggests knitr, rmarkdown, testthat, BiocStyle(>= 2.5.19), MsBackendMgf
Linking To
Depends On Me
Imports Me MetaboAnnotation
Suggests Me AHMassBank, AnnotationHub
Links To Me
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Package Archives

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

Source Package CompoundDb_1.8.0.tar.gz
Windows Binary
macOS Binary (x86_64) CompoundDb_1.8.0.tgz
macOS Binary (arm64) CompoundDb_1.8.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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