Data were collected on a research platform based upon a SYNAPT G2-Si instrument where the standard T-Wave IM device is replaced by a cyclic ion mobility (cIM) separator. The cIM has multiple benefits: the circular path minimises instrument footprint whilst providing a longer, higher mobility resolution separation path; a multi-pass capability provides significantly higher IM resolution over a reduced (selected) mobility range; the device can be enabled for mobility separation or by-passed and the ion entry/exit array can selectively eject species. The cIM device consists of a 100 cm path length RF ion guide which provides mobility separation. MS and tandem MS data were obtained on precursor and product ion separated lipids, respectively, followed by TOF mass measurement. Unsaturated free fatty acid (FA) standards, differing in chain length and number of cis/trans conformations, were chosen to determine the degree of IM separation required to separate lipid isomers. FAs represent the simplest class of lipid components and are a core structural component of each lipid category. In direct infusion cIM-MS measurements FAs with cis-double bond orientations, introduced as two component mixtures, were found to be more compact than those with trans-orientations. Moreover, the cis- and trans-orientations for the monounsaturated FA’s were distinguishable. A different number of cycles through the cIM separator were required to achieve a similar degree of IM separation for mono unsaturated FAs of differing chain length. Unsaturated FAs with two or more double bonds, separated by two mid-chain carbons, could not be distinguished.