As part of the data filtering process, we additionally removed molecules with rare atom species, that is species that appeared in less than 30 molecules. Specifically, we excluded molecules with the following atoms: Co, Fe, Se, As, Si, B, Sn, Au, Cu. We also did not make use of the data corresponding to peptides since the goal of this work is to identify structures of small molecules. Finally, we filtered out all molecules for which the retained spectra, for the selected precursor ions and energies, did not have peaks with m/z > 500. The reason for this final constraint is explained in the following paragraph (Data representation).