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Automated Optimization of XCMS Data Processing parameters

Bioconductor version: Release (3.19)

The outcome of XCMS data processing strongly depends on the parameter settings. IPO (`Isotopologue Parameter Optimization`) is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. IPO uses natural, stable 13C isotopes to calculate a peak picking score. Retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models.

Author: Gunnar Libiseller <Gunnar.Libiseller at>, Christoph Magnes <christoph.magnes at>, Thomas Lieb <thomas.r.lieb at>

Maintainer: Thomas Lieb <thomas.r.lieb at>

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


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:

XCMS Parameter Optimization with IPO HTML R Script
Reference Manual PDF


biocViews ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version 1.30.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL (>= 2) + file LICENSE
Depends xcms(>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats, utils
Imports BiocParallel
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Suggests RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr
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Enhances parallel
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Source Package IPO_1.30.0.tar.gz
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