Gonyautoxins are potent natural neurotoxic analogues of saxitoxin. Due to their biological activity and submilligram lethal dose for man, fast and efficient methods are required for their characterization. Recent advances in ion mobility-mass spectrometry (IM-MS) showed that differentiation of isomers could be achieved using specific experimental conditions involving particular buffer gases as well as cationic species. In this work, IM-MS experiments were carried out using alkali metal ions (Met = Li+, Na+ or K+) and different buffer gases (N2, N2O and CO2) to improve the differentiation of gonyautoxin isomers. The separation of [GTX + Met]+ ion was achieved for GTX2/3 and GTX1/4 from their Na or K adducts. For dcGTX2/3, the ion mobility separation can only be obtained with peak to peak resolution (Rp-p) close to 1 from the [GTXs + Met − H2O]+ species. To understand the gas phase conformation of the different diastereomers, density functional theory (DFT) calculations were performed. IM separation, and collision cross sections on [GTXs + Met]+ and [GTXs + Met − H2O]+ are reported for the first time.