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Workflow to process tandem MS files and build MassBank records

Bioconductor version: Release (3.19)

Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Author: Michael Stravs, Emma Schymanski, Steffen Neumann, Erik Mueller, with contributions from Tobias Schulze

Maintainer: RMassBank at Eawag <massbank at>

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


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:

RMassBank: Non-standard usage HTML R Script
RMassBank: The workflow by example HTML R Script
Reference Manual PDF


biocViews Bioinformatics, ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version 3.14.0
In Bioconductor since BioC 2.11 (R-2.15) (12 years)
License Artistic-2.0
Depends Rcpp
Imports XML, rjson, S4Vectors, digest, rcdk, yaml, mzR, methods, Biobase, MSnbase, httr, enviPat, assertthat, logger, readJDX, webchem, ChemmineR, ChemmineOB, R.utils, data.table, glue
System Requirements OpenBabel
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Suggests BiocStyle, gplots, RMassBankData(>= 1.33.1), xcms(>= 1.37.1), CAMERA, RUnit, knitr, rmarkdown
Linking To
Depends On Me
Imports Me
Suggests Me RMassBankData
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package RMassBank_3.14.0.tar.gz
Windows Binary
macOS Binary (x86_64) RMassBank_3.14.0.tgz
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
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