Separation of nitrogen containing heterocyclic aromatic compounds in oil products is challenging due to the high number of structural isomers. Resolving these isomers is a major challenge in chromatography, even when combined with mass spectrometry (MS), because they have similar volatility, polarity, and mass spectra. Ion-mobility spectrometry (IMS) can address this problem by separating molecules according to their “bulkiness”. When used in combination with mass spectrometry on multiple samples, three-way arrays can be generated which can be modelled by a PARAFAC model to further enhance the resolution. In the three-way case, PARAFAC components cannot be uniquely resolved if the compounds they represent have the same profile in one of the modes. The PARALIND model – i.e., PARAFAC with Linear Dependencies, partly copes with this problem by introducing a dependency matrix. PARAFAC and PARALIND were tested to extract the signals of ten nitrogen containing heterocyclic aromatic compounds from IMS-MS data. The mixtures included three pairs of isomers, which could not be fully resolved by optimization of the ion mobility parameters. The results indicate that ion mobility combined with PARAFAC or PARALIND is a powerful complementary analysis platform that could aid the analysis of products containing a mixture of isomeric hetero-atomic compounds.