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Spectra Infrastructure for Mass Spectrometry Data

Bioconductor version: Release (3.19)

The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.

Author: RforMassSpectrometry Package Maintainer [cre], Laurent Gatto [aut] , Johannes Rainer [aut] , Sebastian Gibb [aut] , Philippine Louail [aut] , Jan Stanstrup [ctb] , Nir Shahaf [ctb], Mar Garcia-Aloy [ctb]

Maintainer: RforMassSpectrometry Package Maintainer <maintainer at>

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


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 new `MsBackend` class HTML R Script
Description and usage of Spectra object HTML R Script
Large-scale data handling and processing with Spectra HTML R Script
Reference Manual PDF


biocViews Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 1.14.1
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends R (>= 4.0.0), S4Vectors, BiocParallel, ProtGenerics(>= 1.35.4)
Imports methods, IRanges, MsCoreUtils(>= 1.7.5), graphics, grDevices, stats, tools, utils, fs, BiocGenerics, MetaboCoreUtils
System Requirements
Bug Reports
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Suggests testthat, knitr (>= 1.1.0), msdata(>= 0.19.3), roxygen2, BiocStyle(>= 2.5.19), mzR(>= 2.19.6), rhdf5(>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick
Linking To
Depends On Me hdxmsqc, MetCirc, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql
Imports Me CompoundDb, MetaboAnnotation, MsExperiment, MsQuality, xcms
Suggests Me MetNet, MsDataHub, PSMatch, RaMS
Links To Me
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Package Archives

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

Source Package Spectra_1.14.1.tar.gz
Windows Binary
macOS Binary (x86_64) Spectra_1.14.1.tgz
macOS Binary (arm64) Spectra_1.14.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
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Old Source Packages for BioC 3.19 Source Archive