The yields of post-source decay (PSD) and time-resolved photodissociation (PD) at 193 and 266 nm were measured for singly protonated leucine enkephalin ([YGGFL ϩ H] ϩ ), a benchmark in the study of peptide ion dissociation, by using tandem time-of-flight mass spectrometry. The peptide ion was generated by matrix-assisted laser desorption ionization (MALDI) using 2,5-dihydroxybenzoic acid as the matrix. The critical energy (E 0 ) and entropy (⌬S ‡ at 1000 K) for the dissociation were determined by Rice-Ramsperger-Kassel-Marcus fit of the experimental data. MALDI was done for a mixture of YGGFL and Y 6 and the plume temperature determined by the kinetic analysis of [Y 6 ϩ H] ϩ data were used to improve the precision of E 0 and ⌬S ‡ for [YGGFL ϩ H] ϩ . E 0 and ⌬S ‡ thus determined (E 0 ϭ 0.67 Ϯ 0.08 eV, ⌬S ‡ ϭ Ϫ24.4 Ϯ 3.2 eu with 1 eu ϭ 4.184 J K Ϫ1 mol Ϫ1 ) were significantly different from those determined by blackbody infrared radiative dissociation (BIRD) (E 0 ϭ 1.10 eV, ⌬S ‡ ϭ Ϫ14.9 eu), and by surface-induced dissociation (SID) (E 0 ϭ 1.13 eV, ⌬S ‡ ϭ Ϫ10.3 eu). Analysis of the present experimental data with the SID kinetics (and BIRD kinetics also) led to an unrealistic situation where not only PSD and PD but also MALDI-TOF signals could not be detected. As an explanation for the discrepancy, it was suggested that transition-state switching occurs from an energy bottleneck (SID/BIRD) to an entropy bottleneck (PSD/PD) as the internal energy increases. (J Am Soc Mass Spectrom 2010, 21, 1151-1158) © 2010 Published by Elsevier Inc. on behalf of American Society for Mass Spectrometry T andem mass spectrometry-detection of product ions from a mass-selected precursor ion-for peptide ions is widely used for protein sequencing [1,2]. Importance of this method has led to active investigation of the dissociation mechanisms of peptide ions [3][4][5]. Attempts [6 -8] have also been made to understand the details of the reaction paths leading to major product ions such as b-and y-type ions, which include the quantum chemical search [9 -11] for the reaction paths. There are not many reports on the dissociation kinetics of peptide ions, even though the information available from such studies will be useful for detailed understanding of the process. Williams and coworkers reported kinetic and dynamic data for some peptide ions determined by blackbody infrared radiative dissociation (BIRD) [12][13][14]. Laskin and coworkers reported similar data obtained by analyzing time-and energy-resolved surface-induced dissociation (SID) [15,16] yields.Recently, we developed a time-resolved photodissociation (PD) method [17][18][19][20][21] to study dissociation kinetics of peptide ions generated by matrix-assisted laser desorption ionization (MALDI) using a tandem time-offlight (TOF) mass spectrometer equipped with a reflectron analyzer. A peptide ion beam was irradiated by a UV laser (193 and 266 nm) pulse at the first timefocusing position of the instrument and product ions formed by PD were analyzed by the reflectron. To obtain t...