The computed spectrum reproduces well all of the observed features except the hydrogenbonded NH stretches, which are typically not well represented by harmonic potentials and thus require more sophisticated treatments to accurately reproduce. Turning to the protonated complex, we find that the spectrum is notably harder to parse by inspection. The free OH feature is preserved, but a new feature near 3400 cm -1 appears, and the fingerprint region is dominated by a complex feature spanning 700 -1600 cm -1 . This type of feature is common to systems in which a shared proton contributes intensity to a variety of mixed modes, while the energy of the center of this broad feature is indicative of the degree to which the proton is shared between the two oxygen atoms. We attribute the 3400 cm -1 feature to tag-induced red shifting of the OH stretch, as the degree of the shift is comparable to previously observed N 2 -bound OH stretches. The broad, lower energy feature is qualitatively consistent with the computed spectrum at the bottom of Figure , though the harmonic spectrum predictably does not reproduce the complexity of the experimental spectrum (Figure ). We ascribe this feature to a series of anharmonic bands sharing intensity with a strongly-shared proton stretch centered around 1200 cm -1 . Such spectral congestion is commonly observed when a strongly absorbing transition is red shifted into resonance with nominally spectroscopically-dark transitions to which it is strongly coupled. The spectrum and degree of shift is consistent with observed shared protons between two deprotonated carboxylic acids in dodecanedioic acid. Taken together, these spectra confirm the possibility that the fully protonated acid can still behave as a base, particularly when confined in a geometry that exposes a binding site bridging the two carboxylic acid carbonyls. This observation adds to the growing library of unintuitive acid base interactions for confined systems confirmed spectroscopically. We found that marginally increasing the "harshness" of the ion source by increasing the pressure in the first vacuum region and creating larger potential differences between adjacent electrodes led to the production of additional fragments in conditions that we would not expect fragmentation for typical ESI-sourced molecular ions. We investigated the formation of these fragments using a series of CID experiments. AA(NH + 4 ) or AAH + was isolated in the LTQ ion trap and fragmented. The same results were found regardless of the species initially isolated, but most experiments discussed here isolated the protonated species initially due to its higher abundance. The primary fragment was then isolated, and fragmented in the same manner until a fragment was created that required significantly higher NCE to dissociate. The resulting mass spectra are shown in Figure . We found dissociation to occur at relatively low NCE more typical of breaking hydrogen bonds (a setting of 10-20 in our instrument). Dissociation proceeds primarily by sequential loss of two water molecules. This observation is unexpected, as there are only three hydrogen atoms bound to oxygen. Therefore, at least one of the water fragments must contain a hydrogen that originated on the CH backbone. Fragmentation of the second water-loss product leads primarily to loss of CO, terminating the dissociation mechanism for low-NCE excitation. A minor pathway is observed consisting of loss of CO after the loss of only one water, and the fragment produced by CO loss subsequently loses water. Thus, both pathways ultimately converge after the loss of two water molecules and one CO group. ) and AAH + are largely similar, suggesting similar overall structure, the three fragments show substantial spectral changes, suggest significant structural rearrangements occur during the dissociation process.