FIORA: Local neighborhood-based prediction of compound mass spectra from single fragmentation events

Yannek Nowatzky, Francesco Friedrich Russo, Jan Lisec, Alexander Kister, Knut Reinert, Thilo Muth and Philipp Benner ()
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Yannek Nowatzky: Federal Institute for Materials Research and Testing (BAM)
Francesco Friedrich Russo: Federal Institute for Materials Research and Testing (BAM)
Jan Lisec: Federal Institute for Materials Research and Testing (BAM)
Alexander Kister: Federal Institute for Materials Research and Testing (BAM)
Knut Reinert: Freie Universität Berlin
Thilo Muth: Freie Universität Berlin
Philipp Benner: Federal Institute for Materials Research and Testing (BAM)

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract Non-targeted metabolomics holds great promise for advancing precision medicine and biomarker discovery. However, identifying compounds from tandem mass spectra remains a challenging task due to the incomplete nature of spectral reference libraries. Augmenting these libraries with simulated mass spectra can provide the necessary references to resolve unmatched spectra, but generating high-quality data is difficult. In this study, we present FIORA, an open-source graph neural network designed to simulate tandem mass spectra. Our main contribution lies in utilizing the molecular neighborhood of bonds to learn breaking patterns and derive fragment ion probabilities. FIORA not only surpasses state-of-the-art fragmentation algorithms, ICEBERG and CFM-ID, in prediction quality, but also facilitates the prediction of additional features, such as retention time and collision cross section. Utilizing GPU acceleration, FIORA enables rapid validation of putative compound annotations and large-scale expansion of spectral reference libraries with high-quality predictions.

Date: 2025
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DOI: 10.1038/s41467-025-57422-4

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