Can ion mobility mass spectrometry and density functional theory help elucidate protonation sites in 'small' molecules?

RATIONALE Ion mobility spectrometry-mass spectrometry (IMS-MS) offers an opportunity to combine measurements and/or calculations of the collision cross-sections and subsequent mass spectra with computational modelling in order to derive the three-dimensional structure of ions. IMS-MS has previously been reported to separate two components for the compound norfloxacin, explained by protonation on two different sites, enabling the separation of protonated isomers (protomers) using ion mobility with distinguishable tandem mass spectrometric (MS/MS) data. This study reveals further insights into the specific example of norfloxacin and wider implications for ion mobility mass spectrometry. METHODS Using a quadrupole ion mobility time-of-flight mass spectrometer, the IMS and MS/MS spectra of norfloxacin were recorded and compared with theoretical calculations using molecular modelling (density functional theory), and subsequent collision cross-section calculations using projection approximation. RESULTS A third significant component in the ion mobilogram of norfloxacin was observed under similar experimental conditions to those previously reported. The presence of the new component is convoluted by co-elution with another previously observed component. CONCLUSIONS This case demonstrates the potential of combined IMS-MS/MS with molecular modelling information for increased understanding of 'small-molecule' fragmentation pathways.