Collision cross section (CCS, Ω) values determined by ion mobility mass spectrometry (IM-MS) provide the study of ion shape in the gas phase and use of these as further identification criteria in analytical approaches. Databases of CCS values for a variety of molecules determined by different instrument types are available. In this study, the comparability of CCS values determined by a drift tube ion mobility mass spectrometer (DTIM-MS) and a traveling wave ion mobility mass spectrometer (TWIM-MS) was investigated to test if a common database could be used across IM techniques. A total of 124 substances were measured with both systems and CCS values of [M + H]+ and [M + Na]+ adducts were compared. Deviations <1% were found for most substances, but some compounds show deviations up to 6.2%, which indicate that CCS databases cannot be used without care independently from the instrument type. Additionally, it was found that for several molecules [2M + Na]+ ions were formed during electrospray ionization, whereas a part of them disintegrates to [M + Na]+ ions after passing through the drift tube and before reaching the TOF region, resulting in two signals in their drift spectrum for the [M + Na]+ adduct. Finally, the impact of different LC-IM-MS settings (solvent composition, solvent flow rate, desolvation temperature, and desolvation gas flow rate) were investigated to test whether they have an influence on the CCS values or not. The results showed that these conditions have no significant impact. Only for karbutilate changes in the drift spectrum could be observed with different solvent types and flow rates using the DTIM-MS system, which could be caused by the protonation at different sites in the molecule.