The quadruplex DNA (qDNA) (dT2G5T)4, (dG4T4G4)2, and the intramolecular d[G3(T2AG3)3] (Q4, Q2 and Q1, respectively), were analysed using circular dichroism (CD) spectroscopy and electrospray ionisation travelling wave ion mobility mass spectrometry (ESI-TWIMS). The CD spectra of the three qDNAs showed, in agreement with the literature, that in ammonium acetate, pH 7.0, Q4 exhibited a parallel strand orientation while Q2 and Q1 were predominantly anti-parallel qDNA. At high concentrations of Q2, the CD spectrum was consistent with a mixture of anti-parallel and parallel forms. ESI-travelling wave ion mobility mass spectra of the qDNA sequences were compared under solution conditions where they were known to be stable and under conditions where they were known to be destabilised (low ammonium acetate concentration with acetonitrile present). This comparison enabled the distinction of ions of the same mass-to-charge that corresponded to single-stranded (ss)Q2, [(dG4T4G4)], or bimolecular Q2, [(dG4T4G4)2]. The resolution of the ESI-TWIMS instrument was sufficient to determine that the ions carrying four and five negative charges most likely arose from the folded intramolecular qDNA, Q1, while the ion carrying six negative charges most likely arose from unfolded Q1. This work shows the utility of ESI-TWIMS in distinguishing among different conformations and structures of qDNA.