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Updated: Nov 2, 2025
Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS
Published on: March 14, 2013
peakPantheR, an R package for large-scale targeted extraction and integration of annotated metabolic features in
Arnaud M Wolfer1,2, Gonçalo D S Correia1,3, Caroline J Sands1,3
1National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, IRDB Building, London W12 0NN, UK.
Summary:
Untargeted liquid chromatography-mass spectrometry (LC-MS) profiling assays are capable of measuring thousands of chemical compounds in a single sample, but unreliable feature extraction and metabolite identification remain considerable barriers to their interpretation and usefulness. peakPantheR (Peak Picking and ANnoTation of High-resolution Experiments in R) is an R package for the targeted extraction and integration of annotated features from LC-MS profiling experiments. It takes advantage of chromatographic and spectral databases and prior information of sample matrix composition to generate annotated and interpretable metabolic phenotypic datasets and power workflows for real-time data quality assessment.
Availability And Implementation:
peakPantheR is available via Bioconductor (https://bioconductor.org/packages/peakPantheR/). Documentation and worked examples are available at https://phenomecentre.github.io/peakPantheR.github.io/ and https://github.com/phenomecentre/metabotyping-dementia-urine.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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