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

Author

Listed:
  • Giovanni Andrea Vitale

    (University of Tübingen)

  • Shu-Ning Xia

    (University of Tübingen)

  • Kai Dührkop

    (Friedrich Schiller University Jena
    Bright Giant GmbH)

  • Mohammad Reza Zare Shahneh

    (University of California Riverside)

  • Heike Brötz-Oesterhelt

    (University of Tübingen
    Partner Site Tübingen
    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
    University of Vienna)

  • Sebastian Böcker

    (Friedrich Schiller University Jena)

  • Robin Schmid

    (Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
    mzio GmbH)

  • Mingxun Wang

    (University of California Riverside)

  • Chambers C. Hughes

    (University of Tübingen
    Partner Site Tübingen
    University of Tübingen)

  • Daniel Petras

    (University of Tübingen
    University of California Riverside)

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.

Suggested Citation

  • 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. , 2025. "Enhancing tandem mass spectrometry-based metabolite annotation with online chemical labeling," Nature Communications, Nature, vol. 16(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61240-z
    DOI: 10.1038/s41467-025-61240-z
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    References listed on IDEAS

    as
    1. Nicholas J. Morehouse & Trevor N. Clark & Emily J. McMann & Jeffrey A. Santen & F. P. Jake Haeckl & Christopher A. Gray & Roger G. Linington, 2023. "Annotation of natural product compound families using molecular networking topology and structural similarity fingerprinting," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    2. Robin Schmid & Daniel Petras & Louis-Félix Nothias & Mingxun Wang & Allegra T. Aron & Annika Jagels & Hiroshi Tsugawa & Johannes Rainer & Mar Garcia-Aloy & Kai Dührkop & Ansgar Korf & Tomáš Pluskal & , 2021. "Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    3. Homa MohammadiPeyhani & Jasmin Hafner & Anastasia Sveshnikova & Victor Viterbo & Vassily Hatzimanikatis, 2022. "Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
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