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LC-MS and GC-MS Data Analysis

Bioconductor version: Release (3.19)

Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.

Author: Colin A. Smith [aut], Ralf Tautenhahn [aut], Steffen Neumann [aut, cre] , Paul Benton [aut], Christopher Conley [aut], Johannes Rainer [aut] , Michael Witting [ctb], William Kumler [aut] , Philippine Louail [aut] , Pablo Vangeenderhuysen [ctb] , Carl Brunius [ctb]

Maintainer: Steffen Neumann <sneumann at>

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


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:

Grouping FTICR-MS data with xcms HTML R Script
LC-MS data preprocessing and analysis with xcms HTML R Script
LC-MS feature grouping HTML R Script
LC-MS/MS data analysis with xcms HTML R Script
Reference Manual PDF


biocViews ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version 4.2.2
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License GPL (>= 2) + file LICENSE
Depends R (>= 4.0.0), BiocParallel(>= 1.8.0)
Imports MSnbase(>= 2.29.3), mzR(>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics(>= 1.35.4), lattice, MassSpecWavelet(>= 1.66.0), S4Vectors, IRanges, SummarizedExperiment, MsCoreUtils(>= 1.15.5), MsFeatures, MsExperiment(>= 1.5.4), Spectra(>= 1.13.7), progress, jsonlite, RColorBrewer, MetaboCoreUtils(>= 1.11.2)
System Requirements
Bug Reports
See More
Suggests BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata(>= 0.25.1), ncdf4, testthat (>= 3.1.9), pander, rmarkdown, MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal, mgcv
Linking To
Enhances Rgraphviz, rgl
Depends On Me CAMERA, flagme, IPO, LOBSTAHS, metaMS, ncGTW, faahKO, PtH2O2lipids
Imports Me CAMERA, cosmiq
Suggests Me CluMSID, msPurity, RMassBank, msdata, mtbls2, RforProteomics, CorrectOverloadedPeaks, enviGCMS, isatabr, LCMSQA, MetabolomicsBasics, RAMClustR
Links To Me
Build Report Build Report

Package Archives

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

Source Package xcms_4.2.2.tar.gz
Windows Binary
macOS Binary (x86_64) xcms_4.2.1.tgz
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive