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Metabolite and small molecule identification via tandem mass spectrometry (MS/MS) involves matching experimental spectra with prerecorded spectra of known compounds. This process is hindered by the current lack of comprehensive reference spectral libraries. To address this gap, we need accurate  in silico  fragmentation tools for predicting MS/MS spectra of compounds for which empirical spectra do not exist. Here, we present SingleFrag, a novel deep learning tool that predicts individual fragments separately, rather than attempting to predict the entire fragmentation spectrum at once. Our results demonstrate that SingleFrag surpasses state-of-the-art  in silico  fragmentation tools, providing a powerful method for annotating unknown MS/MS spectra of known compounds. As a proof of concept, we successfully annotate three previously unidentified compounds frequently found in human samples.

SingleFrag: a deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation