Research in clinical metabolomics

Our group specializes in research and development of population size mass spectrometry-based metabolomics approaches for predictive, personalized, and preventive diagnostics in early life using the massive sample resource available from the Danish National Biobank.

Focus and mission

Our mission is to establish cutting edge mass spectrometry-based metabolomics methods for better understanding of disease etiology and diagnosis in early life.

Analytical methods

We strive to develop high-resolution, fast mass spectrometry-based analytical methods suitable for measurement of population size cohorts. Our analytical focus is on liquid chromatography combined with high resolution tandem mass spectrometry (LC-MS/MS).

Computational methods

Current metabolomics data analysis workflows pose limitations to population size cohorts. Thus, we strive to develop fast computational solutions for the analysis of population size mass spectrometry-based metabolomics data. For chemical structural annotation and biological interpretation of our data we work with diverse metabolome mining tools (e.g. GNPS, MS2LDA, Sirius, MZmine3).

Sample types

Our main focus is on neonatal dried blood spots, whereof over 2 million are currently stored at the Danish Neonatal Screening Biobank. This vast population-based sample resource fosters unique opportunities for our research, but we also work with other clinical and biobanked sample types, such as serum or plasma.


We work in close collaboration with national and international research groups, universities and centers of excellence at the interphase of personalized medicine, metabolomics, microbiome and register-based research and epidemiology.


Our group is involved in diverse teaching activities within Denmark and internationally. We have hosted the 3rd International Summer School on Non-Targeted Metabolomics Data Mining for Biomedical research in 2023 at Statens Serum Institut in collaboration with Aarhus University and the University of Tübingen. Videos of all teaching sessions are publicly available at YouTube.

Selected Publications

Madeleine Ernst


Madeleine Ernst , Congenital Disorders / Metabolomics
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