The fragmentation of peptide ions in tandem mass spectrometry requires intra-molecular migration of “mobile” protons, presumably involving transfer from the most basic site on the peptide backbone to the site of amide bond cleavage.  We investigated the collision-induced dissociation (CID) of protonated hippuric acid (benzoic acid-glycine), nicotinic acid-glycine, isonicotinic acid-glycine, picolinic acid-glycine, acetyl-glycine and glycine-glycine.  The respective pyridine carboxylic acids were used to introduce a basic pyridyl group to serve as the initial protonation site.  The benzoic acid version served as a control.  The question addressed was whether the basic pyridyl groups would sequester the migratory proton and suppress a key dissociation pathway by limiting the potential for proton transfer.  The specific dissociation reaction investigated was the loss of water, which generates a product ion analogous to those used in to identify peptides and proteins by tandem mass spectrometry.  We found that despite the presence of the basic pyridyl group, and a lack of a potential rearrangement reaction to transfer the proton across the peptide backbone in many cases, the dissociation reaction was induced easily.  This result suggests that the dissociation of these model peptides might occur through a heterogenous population of protonated precursor ions, with those involving protonatation of amide carbonyl groups leading to product ions.  The CID results will be presented along with density-functional theory calculations conducted to identify the most probable conformation of the potential precursor ions and the respective transition state and product ion conformation and energies.