Ionic liquids are now used in applications ranging from chemical synthesis to spacecraft propulsion. With this comes the need to characterize new syntheses, identify environmental contamination, and determine eventual fate in terrestrial and space environments. This work investigates the effects of source conditions, particularly capillary temperature, on the observed mass spectrum and determines the collision-induced dissociation (CID) patterns of imidazolium-based ionic liquid cations as a function of their substituent types. Experiments were carried out on a Thermo LTQ-XL ion-trap mass spectrometer and a Bruker microTOF-Q II mass spectrometer. Dissociation of the imidazolium cations occurred predominantly via substituent losses, except in benzyl-substituted systems, for which the neutral loss of the imidazole was exclusively observed. Several of these dissociation pathways were studied in greater depth using complementary quantum chemical calculations. The nature of the neutral losses from the substituents was found to be highly dependent upon the nature of the substituent, as would be expected, establishing bases for characterization.