Simulating Tandem Mass Spectra for Small Molecules using a General-Purpose Large-Language Model

Nguyen, T.; Barupal, D.

doi:10.1101/2025.11.10.687298

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bioRxiv · 10.1101/2025.11.10.687298

Simulating Tandem Mass Spectra for Small Molecules using a General-Purpose Large-Language Model

Nguyen, T.·Barupal, D.

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Abstract

We show a practical application of the Google Gemini large-language-model for simulating tandem mass spectra for compounds from the Blood Exposome Database. This approach bypasses the need for domain-specific model training, suggesting that the chemical fragmentation knowledge could be latently encoded within the Gemini model. General-purpose LLMs represent a useful and accessible tool for expanding in-silico spectral libraries and may accelerate the compound annotation in mass spectrometry-based metabolomics and exposomics.

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Nguyen, T., Barupal, D.. 2025-11-11. Simulating Tandem Mass Spectra for Small Molecules using a General-Purpose Large-Language Model. https://doi.org/10.1101/2025.11.10.687298

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