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Abstract MotivationTandem mass spectrometry is an essential technology for characterizing chemical compounds at high sensitivity and throughput, and is commonly adopted in many fields. However, computational methods for automated compound identification from their MS/MS spectra are still limited, especially for novel compounds that have not been previously characterized. In recent years, in silico methods were proposed to predict the MS/MS spectra of compounds, which can then be used to expand the reference spectral libraries for compound identification. However, these methods did not consider the compounds’ 3D conformations, and thus neglected critical structural information. ResultsWe present the 3D Molecular Network for Mass Spectra Prediction (3DMolMS), a deep neural network model to predict the MS/MS spectra of compounds from their 3D conformations. We evaluated the model on the experimental spectra collected in several spectral libraries. The results showed that 3DMolMS predicted the spectra with the average cosine similarity of 0.691 and 0.478 with the experimental MS/MS spectra acquired in positive and negative ion modes, respectively. Furthermore, 3DMolMS model can be generalized to the prediction of MS/MS spectra acquired by different labs on different instruments through minor fine-tuning on a small set of spectra. Finally, we demonstrate that the molecular representation learned by 3DMolMS from MS/MS spectra prediction can be adapted to enhance the prediction of chemical properties such as the elution time in the liquid chromatography and the collisional cross section measured by ion mobility spectrometry, both of which are often used to improve compound identification. Availability and implementationThe codes of 3DMolMS are available at https://github.com/JosieHong/3DMolMS and the web service is at https://spectrumprediction.gnps2.org.