A pure amphiphilic macrocrown ether (MC-12) was obtained by removing linear oligomers and larger macrocycles at the macrocyclization step, before proceeding with an established synthetic procedure. This pure MC-12 was used to synthesize a rotaxane composed of one MC-12 ring threaded with one end-capped poly(tetrahydrofuran) (PTHF) oligomer by equilibrating half an equivalent of the thread with an organized solution of MC-12 and end-capping the threads with excess 2-p-[tris(p-tert-butylphenyl)methyl]phenoxymethyl-4,4-dimethylazlactone. The rotaxane was positively identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry (MS), although the spectra showed a low abundance of the rotaxane ions and high abundances of unthreaded MC-12 and end-capped thread ions in the product isolated from the threading experiment. Analysis by GPC was inconclusive because both the rotaxane and a one-to-one complex elute at the same retention volume. MALDI-ToF and electrospray ionization quadrupole ion trap (ESI-QIT) MS analyses of the rotaxane sample and mixtures of MC-12 and end-capped thread, including studies using varying laser intensities, comparisons of linear and reflectron analysis modes of the ToF MS, and analysis of the rotaxane by the post-source decay method demonstrated that the rotaxane does not fragment during the MALDI-ToF MS analysis, although the rotaxane ionizes less efficiently than either of its two components. HPLC using silica columns and an eluant of THF with 0.3 wt % Aliquat 336 confirmed that a “further-purified” sample of the rotaxane mixture was composed of 66 wt % end-capped thread, 23 wt % MC-12, and 11 wt % rotaxane, in qualitative agreement with the corresponding MALDI-ToF mass spectrum.