Liquid chromatography tandem mass spectrometry (LC-MS/MS), a widely used method for comparative 'omics analysis, experiences challenges with compound identification due to matrix effects, difficulty in separating isomer and isobaric ions, and long analysis times. Ion mobility spectrometry (IMS) has proven to be useful in separating isomer and isobar ions; however, IMS-MS suffers from decreased peak capacity due to the correlation in ion size and mass. In proof-of-principle experiments, the use of gas-phase hydrogen/deuterium exchange (HDX) combined with IMS-MS/MS techniques is demonstrated to offer advantages for compound identification. Measurements providing unique information for ions include m/z value, drift time in He buffer gas, drift time in He and D2O buffer gases, deuterium incorporation pattern (isotopic distribution), deuterium incorporation pattern after collisional activation, and fragment ion deuterium incorporation pattern upon collision-induced dissociation (CID). These techniques are here shown to be highly reproducible (drift time coefficients of variation < 1.0% and isotopic pattern root-mean-square deviations of 0.5-1.5%) while demonstrating an increased ability to distinguish individual molecules from diverse classes of compounds (peptides, catecholamines, nucleosides, amino acids, etc.). The concept of using such (and similar) information for rapid, high-throughput molecular identification via database searching of standard libraries is briefly discussed, and an example of such usage is presented for a bonafide metabolite extract sample.