Enhancing tandem mass spectrometry-based metabolite annotation with online chemical labeling

Giovanni Andrea Vitale, Shu-Ning Xia, Kai Dührkop, Mohammad Reza Zare Shahneh, Heike Brötz-Oesterhelt, Yvonne Mast, Corinna Brungs, Sebastian Böcker, Robin Schmid, Mingxun Wang, Chambers C. Hughes () and Daniel Petras ()
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Giovanni Andrea Vitale: University of Tübingen
Shu-Ning Xia: University of Tübingen
Kai Dührkop: Friedrich Schiller University Jena
Mohammad Reza Zare Shahneh: University of California Riverside
Heike Brötz-Oesterhelt: University of Tübingen
Yvonne Mast: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures
Corinna Brungs: Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
Sebastian Böcker: Friedrich Schiller University Jena
Robin Schmid: Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
Mingxun Wang: University of California Riverside
Chambers C. Hughes: University of Tübingen
Daniel Petras: University of Tübingen

Nature Communications, 2025, vol. 16, issue 1, 1-9

Abstract: Abstract Metabolite identification in non-targeted mass spectrometry-based metabolomics remains a major challenge due to limited spectral library coverage and difficulties in predicting metabolite fragmentation patterns. Here, we introduce Multiplexed Chemical Metabolomics (MCheM), which employs orthogonal post-column derivatization reactions integrated into a unified mass spectrometry data framework. MCheM generates orthogonal structural information that substantially improves metabolite annotation through in silico spectrum matching and open-modification searches, offering a powerful new toolbox for the structure elucidation of unknown metabolites at scale.

Date: 2025
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DOI: 10.1038/s41467-025-61240-z

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