The internal energy deposited in both on-and off-resonance collisional activation in Fourier transform ion cyclotron resonance mass spectrometry is measured with ion nanocalorimetry and is used to obtain information about the dissociation energy and entropy of a protonated peptide. Activation of Na ϩ (H 2 O) 30 results in sequential loss of water molecules, and the internal energy of the activated ion can be obtained from the abundances of the product ions. Information about internal energy deposition in on-resonance collisional activation of protonated peptides is inferred from dissociation data obtained under identical conditions for hydrated ions that have similar m/z and degrees-of-freedom. From experimental internal energy deposition curves and Rice-Ramsperger-Kassel-Marcus (RRKM) theory, dissociation data as a function of collision energy for protonated leucine enkephalin, which has a comparable m/z and degrees-of-freedom as Na ϩ (H 2 O) 30 , are modeled. The threshold dissociation energies and entropies are correlated for data acquired at a single time point, resulting in a relatively wide range of threshold dissociation energies (1.1 to 1.7 eV) that can fit these data. However, this range of values could be significantly reduced by fitting data acquired at different dissociation times. By measuring the internal energy of an activated ion, the number of fitting parameters necessary to obtain information about the dissociation parameters by modeling these data is reduced and could result in improved accuracy for such methods. [11,12] (ETD) dissociation, have been developed, and each method has its advantages, collisionally activated dissociation (CAD) or collision induced dissociation (CID) remains the most widely used method owing in part to the simplicity and efficiency of implementation, and the extensive structural information that can be rapidly obtained [13][14][15].A critical piece of information necessary to accurately characterize ion dissociation in any activation method is the internal energy that is deposited into the activated ion. For thermal methods, such as highpressure mass spectrometry [16,17] or blackbody infrared radiative dissociation (BIRD) [6, 18 -23], the internal energy of an activated ion is often given by a Boltzmann distribution at a given temperature [18]. With BIRD, large trapped ions can rapidly equilibrate with the blackbody radiation field at low pressure, and their internal energy is given by a Boltzmann distribution at the temperature of their surroundings [18]. By measuring dissociation rate constants as a function of temperature, accurate dissociation activation energies and entropies can be directly obtained for large ions, including proteins [6,20] and macromolecular complexes [21,23].By comparison, the internal energy deposition in CAD can be more difficult to characterize, particularly for large ions, because of uncertainties in how much energy is transferred during collisions between the ions and gaseous atoms or molecules [24,25]. Methods, such as guided ion beam...