Collision induced dissociation (CID) and collision induced unfolding (CIU) experiments are important tools for determining the structures of and differences between biomolecular complexes with mass spectrometry. However, quantitative comparison of CID/CIU data acquired on different platforms or even using different regions of the same instrument can be very challenging due to differences in gas identity and pressure, electric fields, and other experimental parameters. In principle, these can be reconciled by a detailed understanding of how ions heat, cool, and dissociate or unfold in time as a function of these parameters. Fundamental information needed to model these processes for different ion types and masses is their heat capacity as a function of the internal (i.e., vibrational) temperature. Here, we use quantum computational theory to predict average heat capacities as a function of temperature for a variety of model biomolecule types from 100 to 3000 K. On a degree-of-freedom basis, these values are remarkably invariant within each biomolecule type and can be used to estimate heat capacities of much larger biomolecular ions. We also explore effects of ion heating, cooling, and internal energy distribution as a function of time using a home-built program (IonSPA). We observe that these internal energy distributions can be nearly Boltzmann for larger ions (greater than a few kDa) through most of the CID/CIU kinetic window after a brief (few-μs) induction period. These results should be useful in reconciling CID/CIU results across different instrument platforms and under different experimental conditions, as well as in designing instrumentation and experiments to control CID/CIU behavior.
