Analysis types and quantification methods applied in UHPLC-MS metabolomics research: a tutorial

Metabolomics, vol. 20, pp. 95

Abstract

BACKGROUND: Different types of analytical methods, with different characteristics, are applied in metabolomics and lipidomics research and include untargeted, targeted and semi-targeted methods. Ultra High Performance Liquid Chromatography-Mass Spectrometry is one of the most frequently applied measurement instruments in metabolomics because of its ability to detect a large number of water-soluble and lipid metabolites over a wide range of concentrations in short analysis times. Methods applied for the detection and quantification of metabolites differ and can either report a (normalised) peak area or an absolute concentration. AIM OF REVIEW: In this tutorial we aim to (1) define similarities and differences between different analytical approaches applied in metabolomics and (2) define how amounts or absolute concentrations of endogenous metabolites can be determined together with the advantages and limitations of each approach in relation to the accuracy and precision when concentrations are reported. KEY SCIENTIFIC CONCEPTS OF REVIEW: The pre-analysis knowledge of metabolites to be targeted, the requirement for (normalised) peak responses or absolute concentrations to be reported and the number of metabolites to be reported define whether an untargeted, targeted or semi-targeted method is applied. Fully untargeted methods can only provide (normalised) peak responses and fold changes which can be reported even when the structural identity of the metabolite is not known. Targeted methods, where the analytes are known prior to the analysis, can also report fold changes. Semi-targeted methods apply a mix of characteristics of both untargeted and targeted assays. For the reporting of absolute concentrations of metabolites, the analytes are not only predefined but optimized analytical methods should be developed and validated for each analyte so that the accuracy and precision of concentration data collected for biological samples can be reported as fit for purpose and be reviewed by the scientific community.

Authors 10

1. Richard D. Beger

   National Center for Toxicological Research · United States Food and Drug Administration

   Affiliation as printed

   National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA

2. Royston Goodacre

   University of Liverpool

   Affiliation as printed

   Department of Biochemistry, Cell and Systems Biology, Centre for Metabolomics Research, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK

3. Christina M. Jones

   National Institute of Standards and Technology

   Affiliation as printed

   Office of Advanced Manufacturing, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA

4. Katrice A. Lippa

   National Institute of Standards and Technology

   Affiliation as printed

   Office of Weights and Measures, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA

5. Oleg A. Mayboroda Aachen Centre for Proteomics and Metabolomics

   Leiden University · Leiden University Medical Center

   Affiliation as printed

   Center for Proteomics and Metabolomics, Leiden University Medical Centre, Leiden, The Netherlands

6. Donna O’Neill

   University of Birmingham

   Affiliation as printed

   School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, UK

7. Lukáš Najdekr

   Institute of Molecular and Translational Medicine · Palacký University Olomouc

   Affiliation as printed

   Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacký University Olomouc, 779 00, Olomouc, Czech Republic

8. Ioanna Ntai

   BioMarin (United States)

   Affiliation as printed

   BioMarin Pharmaceutical Inc., San Rafael, CA, USA

9. Ian D. Wilson

   University of Liverpool · Imperial College London

   Affiliation as printed

   Computational and Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK

   Department of Biochemistry, Cell and Systems Biology, Centre for Metabolomics Research, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK

10. Warwick B. Dunn corresponding

    University of Liverpool

    Affiliation as printed

    Department of Biochemistry, Cell and Systems Biology, Centre for Metabolomics Research, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK. warwick.dunn@liverpool.ac.uk

    Department of Biochemistry, Cell and Systems Biology, Centre for Metabolomics Research, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK