To install this package, start R and enter:


In most cases, you don't need to download the package archive at all.


LC/MS and GC/MS Data Analysis

Bioconductor version: 2.13

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 <csmith at>, Ralf Tautenhahn <rtautenh at>, Steffen Neumann <sneumann at>, Paul Benton <hpaul.benton08 at>, Christopher Conley <cjconley at>

Maintainer: Ralf Tautenhahn <rtautenh at>

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


To install this package, start R and enter:



To view documentation for the version of this package installed in your system, start R and enter:



PDF FlowChart.pdf
PDF R Script Grouping FTICR-MS data with xcms
PDF R Script Installation Instructions for xcms
PDF R Script LC/MS Preprocessing and Analysis with xcms
PDF R Script Processing Tandem-MS and MS$^n$ data with xcms
PDF   Reference Manual
Text   NEWS


biocViews MassSpectrometry, Metabolomics, Software
Version 1.38.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier
License GPL (>= 2)
Depends R (>= 2.14.0), methods, mzR(>= 1.1.6), BiocGenerics, Biobase
Suggests faahKO, msdata, ncdf, multtest, rgl, MassSpecWavelet(>= 1.5.2), RANN, RUnit
System Requirements
Depends On Me CAMERA, faahKO, flagme
Imports Me CAMERA, Risa
Suggests Me MassSpecWavelet, msdata, RforProteomics, RMassBank

Package Archives

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

Package Source xcms_1.38.0.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) xcms_1.38.0.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center