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Updated: Jun 10, 2026

A Strategy for Sensitive, Large Scale Quantitative Metabolomics
Published on: May 27, 2014
Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data
H Paul Benton1, Elizabeth J Want, Timothy M D Ebbels
1Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Sir Alexander Fleming Building, Imperial College London, London, SW7 2AZ, UK. hpaul.benton08@imperial.ac.uk
Motivation:
High mass accuracy is an important goal in liquid chromatography-mass spectrometry experiments. Some manufacturers employ a mass calibration system that regularly switches between the analyte and a standard reference compound, and leads to gaps in the analyte data. We present a method for correction of such gaps in global molecular profiling applications such as metabolomics. We demonstrate that it improves peak detection and quantification, successfully recovering the expected number of peaks and intensity distribution in an example metabolomics dataset.
Availability And Implementation:
Available in XCMS versions 1.23.3 and higher. Distributed via Bioconductor under GNU General Public License. (http://www.bioconductor.org/packages//2.7/bioc/html/xcms.html).
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