The detection and assignment of protonation isomers, termed protomers, of gas-phase ions remains a challenge in mass spectrometry. With the emergence of ion-mobility techniques combined with tuneable-laser photodissociation spectroscopy, new experimental combinations are possible to now meet this challenge. In this paper, the differences in fragmentation and electronic spectroscopy of singly protonated (S)-nicotine (nicH+) ions are analysed using action spectroscopy in the ultraviolet region and field asymmetric ion mobility spectrometry (FAIMS). Experiments are supported by quantum chemical calculations (DFT, TD-DFT and CC2) of both spectroscopic and thermochemical properties. Electrospray ionisation (ESI) of (S)-nicotine from different solvents leads to different populations of two nicH+ protomers corresponding to protonation on the pyridine nitrogen and pyrrolidine nitrogen, respectively. FAIMS gives partial resolution of these protomers and enables characteristic product ions to be identified for each isomer as verified directly by analysis of product-ion specific action spectroscopy. It is shown that while characteristic, these product ions are not exclusive to each protomer. Calculations of vertical electronic transitions assist in rationalising the photodissociation action spectra. The integration of photodissociation action spectroscopy with FAIMS-mass spectrometry is anticipated to be a useful approach for separating and assigning protonation isomers of many other small molecular ions.