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parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)

Bioconductor version: Release (3.19)

mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.

Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer

Maintainer: Steffen Neumann <sneumann at>

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


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:

Accessin raw mass spectrometry and identification data HTML R Script
Reference Manual PDF


biocViews DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 2.38.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License Artistic-2.0
Depends R (>= 4.0.0), Rcpp (>= 0.10.1), methods, utils
Imports Biobase, BiocGenerics(>= 0.13.6), ProtGenerics(>= 1.17.3), ncdf4
System Requirements C++11, GNU make
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Suggests msdata(>= 0.15.1), RUnit, mzID, BiocStyle(>= 2.5.19), knitr, XML, rmarkdown
Linking To Rcpp, Rhdf5lib(>= 1.1.4)
Depends On Me MSnbase
Imports Me adductomicsR, CluMSID, DIAlignR, MSnID, msPurity, peakPantheR, SIMAT, TargetDecoy, topdownr, xcms, yamss
Suggests Me AnnotationHub, MetaboAnnotation, MsBackendRawFileReader, MsBackendSql, MsDataHub, MsExperiment, MsQuality, PSMatch, qcmetrics, Spectra, msdata, RforProteomics, chromConverter, erah
Links To Me
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Package Archives

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

Source Package mzR_2.38.0.tar.gz
Windows Binary
macOS Binary (x86_64) mzR_2.38.0.tgz
macOS Binary (arm64) mzR_2.38.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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