A novel sample preparation method to probe the solution phase structure of dimerized Gramicidin A (GA) inserted into lipid vesicle bilayers is described. This method, termed vesicle capture-freeze-drying (VCFD), when coupled with electrospray ionization-ion mobility-mass spectrometry (ESI-IM-MS), successfully demonstrates the first evidence for the preservation of membrane-bound structure in the analysis of solution phase conformers retained into the gas phase. The extremely hydrophobic character of GA ensures that only membrane-bound conformations are captured and subsequently monitored when samples are prepared using VCFD, removing a barrier that has prevented previous attempts at direct analysis using mass spectrometry. Solution-phase physicochemical interactions of GA influenced by lipid acyl chain length and extent of acyl chain unsaturation can now be probed by monitoring the conformer preferences using IM-MS. Increasing the acyl chain length from 12 to 22 carbons yields [2GA + 2Na](2+) IM-MS profiles with reduced conformer microheterogeneity. POPC (16:0, 18:1 PC), a lipid possessing a single acyl chain unsaturation point, yields the highest abundance of the single stranded head to head (SSHH) conformer. Conformer preferences adopted in the lipid bilayer are maintained as GA dimers travel from the solution phase to fully desolvated gas-phase ions demonstrating that distributions observed using ESI-IM-MS unambiguously reflect the ensemble of conformers observed in the solution phase. VCFD-ESI-IM-MS yields novel biophysical insight into the influence of lipid bilayer membranes on conformer preferences and conformer heterogeneity of an important channel-forming membrane peptide.