Discovery of metabolites prevails amid in-source fragmentation

Yasin El Abiead^#¹, Adriano Rutz^#², Simone Zuffa¹, Bashar Amer³, Shipei Xing¹, Corinna Brungs⁴, Robin Schmid⁴, Mario S P Correia², Andres Mauricio Caraballo-Rodriguez^{1

5}, Amir Zarrinpar^{6

7

8

9}, Helena Mannochio-Russo¹, Michael Witting^{10

11}, Ipsita Mohanty¹, Tomáš Pluskal⁴, Wout Bittremieux¹², Rob Knight^{8

13}, Andrew D Patterson¹⁴, Justin J J van der Hooft^{15

16}, Sebastian Böcker¹⁷, Warwick B Dunn¹⁸, Roger G Linington¹⁹, David S Wishart²⁰, Jean-Luc Wolfender^{21

22}, Oliver Fiehn²³, Nicola Zamboni², Pieter C Dorrestein^{24

25

26

27}

Affiliations

¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
² Institute for Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
³ Thermo Fisher Scientific, San Jose, CA, USA.
⁴ Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
⁵ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
⁶ Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA.
⁷ Division of Gastroenterology, Jennifer Moreno Department of Veterans Affairs Medical Center, La Jolla, CA, USA.
⁸ Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
⁹ Institute of Diabetes and Metabolic Health, University of California, San Diego, La Jolla, CA, USA.
¹⁰ Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany.
¹¹ Chair of Analytical Food Chemistry, TUM School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany.
¹² Department of Computer Science, University of Antwerp, Antwerp, Belgium.
¹³ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
¹⁴ Department of Biochemistry and Molecular Biology and Department of Veterinary and Biomedical Sciences, the Pennsylvania State University, University Park, PA, USA.
¹⁵ Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.
¹⁶ Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.
¹⁷ Institute of Computer Science, Friedrich Schiller University Jena, Jena, Germany.
¹⁸ Department of Biochemistry, Cell and Systems Biology, Centre for Metabolomics Research, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, UK.
¹⁹ Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
²⁰ Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada.
²¹ Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland.
²² School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.
²³ West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA.
²⁴ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.
²⁵ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.
²⁶ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.
²⁷ Department of Pharmacology, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.

^# Contributed equally.

PMID: 40021935
DOI: 10.1038/s42255-025-01239-4

Discovery of metabolites prevails amid in-source fragmentation

Yasin El Abiead et al. Nat Metab. 2025 Mar.

. 2025 Mar;7(3):435-437.

doi: 10.1038/s42255-025-01239-4.

Authors

Affiliations

¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
² Institute for Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
³ Thermo Fisher Scientific, San Jose, CA, USA.
⁴ Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
⁵ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
⁶ Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA.
⁷ Division of Gastroenterology, Jennifer Moreno Department of Veterans Affairs Medical Center, La Jolla, CA, USA.
⁸ Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
⁹ Institute of Diabetes and Metabolic Health, University of California, San Diego, La Jolla, CA, USA.
¹⁰ Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany.
¹¹ Chair of Analytical Food Chemistry, TUM School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany.
¹² Department of Computer Science, University of Antwerp, Antwerp, Belgium.
¹³ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
¹⁴ Department of Biochemistry and Molecular Biology and Department of Veterinary and Biomedical Sciences, the Pennsylvania State University, University Park, PA, USA.
¹⁵ Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.
¹⁶ Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.
¹⁷ Institute of Computer Science, Friedrich Schiller University Jena, Jena, Germany.
¹⁸ Department of Biochemistry, Cell and Systems Biology, Centre for Metabolomics Research, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, UK.
¹⁹ Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
²⁰ Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada.
²¹ Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland.
²² School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.
²³ West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA.
²⁴ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.
²⁵ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.
²⁶ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.
²⁷ Department of Pharmacology, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.

^# Contributed equally.

PMID: 40021935
DOI: 10.1038/s42255-025-01239-4

No abstract available

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Conflict of interest statement

Competing interests: P.C.D. is an advisor to and holds equity in Cybele, BileOmix and Sirenas and is a scientific co-founder of, is advisor to, holds equity in and/or received income from Ometa, Enveda and Arome with prior approval by the University of California, San Diego. P.C.D. also consulted for DSM Animal Health in 2023. J.J.J.v.d.H. is member of the scientific advisory board of Naicons Srl., Milano, Italy and consults for Corteva Agriscience, Indianapolis, IN, USA. R.S. and T.P. are co-founders of mzio GmbH. A.Z. is a co-founder of and equity holder in Endure Biotherapeutics. R.K. is a scientific advisory board member and consultant for BiomeSense, Inc., has equity and receives income. He is a scientific advisory board member and has equity in GenCirq. He is a consultant for DayTwo and receives income. He has equity in and acts as a consultant for Cybele. He is a co-founder of Biota, Inc., and has equity. He is a cofounder of Micronoma, has equity and is a scientific advisory board member. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. The other authors declare no competing interests. S.B. is co-founder of Bright Giant.

References

1. Giera, M., Aisporna, A., Uritboonthai, W. & Siuzdak, G. Nat. Metab. 6, 1647–1648 (2024).
1. Strachan, J. The dark metabolome: a figment of our fragmentation? Analytical Scientist https://theanalyticalscientist.com/fields-applications/the-dark-metabolo... (2024).
1. Lowe, D. Phantom metabolites? Science https://www.science.org/content/blog-post/phantom-metabolites (2024).
1. Schmid, R. et al. Nat. Commun. 12, 3832 (2021). - DOI - PubMed - PMC
1. Lu, W. et al. Anal. Chem. 92, 11573–11581 (2020). - DOI - PubMed - PMC

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Discovery of metabolites prevails amid in-source fragmentation

Affiliations

Discovery of metabolites prevails amid in-source fragmentation

Authors

Affiliations

Conflict of interest statement

References

Publication types

Grants and funding

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Full Text Sources