There is currently a lack of computational methods supporting the elucidation of unknown compounds by mass spectrometry. In this study, we develop and evaluate seven different protocols, based on the ab initio Roby-Gould bond indices [Gould et al., Theor. Chem. Acc., 2008, 119, 275] for predicting the mass?to?charge ratio of the highest intensity peak (base peak) in electron impact mass spectra. The protocols are applied to a dataset of 75 molecules, including five directly targeted semiochemicals. The Roby-Gould bond indices are also surveyed exhaustively, for the first time, for a dataset of 103 molecules with 682 C?C bonds. For neutral species we find that the bond indices are, as may be expected, highly correlated with the bond length; for cations, although there is a correlation, the bond indices are more variable. One of our protocols, protocol MG, correctly predicts the base peak in the mass spectra for 65 out of 75 cases. The correct base peak was calculated for three out of five targeted natural products.