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Ion mobility spectrometry (IMS) separates ions while they travel through a buffer gas under the influence of an electrical field. The separation is affected by mass and charge but most particularly by shape (collision cross section). When coupled to MS, IMS-MS offers therefore a powerful tool for structural elucidation and isomer separation. Systematic studies aimed to compare and quantitate the effects of structural changes on drift time such as length and ramification of carbon chain, unsaturation, geometrical isomerism (cis/trans isomers for instance), cyclization and ring size are, however, scarce. Herein we used traveling wave ion mobility mass spectrometry (TWIM-MS) to systematically evaluate the relationship between structure and drift time. For that, a series of deprotonated carboxylic acids were used as model ions with a carboxylate “charge tag” for gas phase MS manipulation. Carboxylic acids showed a near linear correlation between the increase of carbon number and the increase of collision cross section (CCS). The number of double bonds changes slightly the CCS of unsaturated acids. No differences in drift time and no significant differences in CCS of cis- and trans-double bond of oleic and elaidic acids were observed. Cyclization considerably reduces the CCS. In cyclic carboxylic acids, the increase of double bonds and aromatization significantly reduces the CCS and the drift times. The use of a more polarizable drift gas, CO2, improved in some cases the separation, as for biomarker isomers of steranoic acids. The β-isomer (cis-decaline) has smaller CCS and therefore displayed lower drift time compared to the α-isomer (trans-decaline). Structural changes revealed by calculations were correlated with trends in drift times.