Comprehensive analysis of ammonia and biogenic amines in ecologically diverse systems with high-resolution mass spectrometry

Fido, M.; Barazzone, E. C.; Hoesli, E.; Scheidegger, J.; Khurana, N.; Kim, J.; Arnoldini, M.; Sperfeld, M.; Schumann, R. L.; Sunagawa, S.; Hausmann, A.; Zenobi, R.; Slack, E. M. C.

doi:10.64898/2026.09.22.753493

bioRxiv · 10.64898/2026.09.22.753493

Comprehensive analysis of ammonia and biogenic amines in ecologically diverse systems with high-resolution mass spectrometry

Fido, M.·Barazzone, E. C.·Hoesli, E.·Scheidegger, J.·Khurana, N.·Kim, J.·Arnoldini, M.·Sperfeld, M.·Schumann, R. L.·Sunagawa, S.·Hausmann, A.·Zenobi, R.·Slack, E. M. C.

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Abstract

The acquisition of sufficient nitrogen for growth, as well as the disposal of highly toxic nitrogen-containing degradation products, represent serious metabolic challenges in all multicellular organisms and microbial ecosystems. Understanding these processes requires a broadly applicable system to accurately quantify the concentration of a wide spectrum of biological amines and inorganic nitrogen-containing compounds. To date, this has been challenging due to limited specificity, selectivity, breadth and/or sensitivity of assays. Here we present a simple, optimized method based on liquid chromatography and high-resolution mass spectrometry, with an accompanying analysis pipeline, for the accurate quantification of more than 30 of these compounds, including ammonia. We demonstrate the effectiveness of this method in quantifying relevant nitrogen-containing compounds in mouse and human gut content, bacterial cultures, algal symbiosis in a cnidarian and freshwater ecosystem samples. As a proof-of-concept, we applied the method to study the influence of the gut microbiome on cecal nitrogen distribution in mice with different gnotobiotic microbiomes. This revealed a profound influence of gut microbiota composition on amino acid, ammonia, and amine concentrations in the upper large intestine. Overall, we provide a broadly applicable approach that can be used across microbial ecology fields to generate novel insights into the biology of nitrogen assimilation, exchange, and disposal.

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Fido, M., Barazzone, E. C., Hoesli, E., Scheidegger, J., Khurana, N., Kim, J., Arnoldini, M., Sperfeld, M., Schumann, R. L., Sunagawa, S., Hausmann, A., Zenobi, R., Slack, E. M. C.. 2026-09-23. Comprehensive analysis of ammonia and biogenic amines in ecologically diverse systems with high-resolution mass spectrometry. https://doi.org/10.64898/2026.09.22.753493

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