Herein, we show a direct link between the observed dissociation energies derived from collision-induced dissociation (CID) mass spectra using RRKM theory and the molecular conformations for 8 different non-specific peptide–saccharide complexes containing either a tri-saccharide (d-(+)-raffinose and d-panose) or tetra-saccharide (stachyose and maltotetraose) with a small peptide (FLEEL and FLEEV). The relative ESI-MS intensities for complexes containing isomeric saccharides were found not to be highly related to the 0K activation energy (E0) calculated using an RRKM-based fitting of CID breakdown diagrams yet, the E0 values were found to be highly related to the overall conformation adopted by the non-covalent complex in the gas phase. Complexes containing peptide FLEE(L/V) with the tri-saccharide raffinose or panose were found to have similar conformations based on molecular mechanics/molecular dynamics (MM/MD) simulations and ion mobility (IMS) drift times. Correspondingly, when complexed with the FLEEL peptide, the tri-saccharides had E0 values of ∼0.64eV. Conversely, complexes containing a FLEE(L/V) peptide with one of the isomeric tetra-saccharides; stachyose or maltotetraose, were found to have quite different MM/MD structures and IMS drift times that differed by 2.4% and 6.3% when in complex with FLEEL and FLEEV, respectively. We suggest that this difference of conformation is a major factor which accounts for the ∼0.08eV higher E0 value for the dissociation of the FLEE(L/V) complexes with stachyose over those with maltotetraose. Also found was that the drift times of unbound isomeric maltotetraose and stachyose are equal however, when complexed with the peptide are quite different, suggesting that distinguishing and identification of these saccharides could be accomplished through IMS measurements of the saccharides in a peptide bound state.