Time-evolution of product ion signals in ultraviolet photodissociation (UV-PD) of singly protonated peptides with an arginine at the N-terminus was investigated by using a tandem time-of-flight mass spectrometer equipped with a cell floated at high voltage. Observation of different time-evolution patterns for different product ion types-an apparently nonstatistical behavior-could be explained within the statistical framework by invoking consecutive formation of some product ions and broad internal energy distributions for precursor ions. a n ϩ 1 and b n ions were taken as the primary product ions from this type of peptide ions. Spectral characteristics in post-source decay, UV-PD, and collisionally activated dissociation at low and high kinetic energies could be explained via rough statistical calculation of rate constants. Specifically, the striking characteristics in high-energy CAD and UV-PD-dominance of a n and d n formed via a n ϩ 1-were not due to the peculiarity of the excitation processes themselves, but due to quenching of the b n channels caused by the presence of arginine. ( T andem mass spectrometry has been widely used for identification and sequence determination of polypeptides and proteins [1][2][3]. In spite of extensive studies made so far, fundamental understanding on the dissociation of activated peptide ions observed by tandem mass spectrometry is still lacking. This is in contrast with the case of the dissociation of small polyatomic ions, for which nearly quantitative theoretical description and even prediction are possible [4]. The main reasons for such a lack of fundamental understanding are experimental and computational difficulties to get structural, mechanistic, and kinetic data for large polyatomic systems consisting of more than 100 atoms. In this regard, it is to be mentioned that we recently developed a systematic method to calculate sequence-specific statistical (Rice-Ramsperger-KasselMarcus, RRKM) rate constants for dissociations of peptide and protein ions [5][6][7].The most popular method to activate a peptide ion and hence to induce its dissociation is the collisionally activated dissociation (CAD) [8 -12]. The kinetic energy of a peptide ion is an important factor affecting the CAD spectral pattern. Hence, CAD of a peptide ion is classified into two categories, low (around 100 eV) and high (higher than 1 keV) energy regimes. In the lowenergy CAD [11], which is typically done with triple quadrupole ion trap and ion cyclotron resonance mass spectrometers, a peptide ion gains sufficient energy for dissociation usually via multiple collisions, each collision supplying rather small amounts of internal energy through vibrational excitation. Most of the product ions are b and y types (see Scheme 1) formed via rearrangement reactions.Presence of arginine, proline and aspartic acid residues and the charge state of a peptide ion are known to affect the relative intensities of these product ions. The "mobile proton" model [13,14] has been devised to explain this. In the high-energy CA...

Product ion yields in postsource decay and time-resolved photodissociation at 193 and 266 nm were measured for some peptide ions with lysine ([KF6 + H]+, [F6K + H]+, and [F3KF3 + H]+) formed by matrix-assisted laser desorption ionization. The critical energy (E0) and entropy (DeltaS(double dagger)) were determined by RRKM fitting of the data. The results were similar to those found previously for peptide ions with histidine. To summarize, the presence of a basic residue, histidine or lysine, inside a peptide ion retarded its dissociation by lowering DeltaS(double dagger). On the basis of highly negative DeltaS(double dagger), presence of intramolecular interaction involving a basic group in the transition structure was proposed.

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A kinetic model was built for the formation ofb and y ions 一 which are the main product ions generated from sin읺y protonated peptides at low internal energy regime -on a microsecond time scale based on the potential energy diagram along the oxazolone pathway reported previously. The rate constants were evaluated using the Rice-Ramsperger-Kassel-Marcus theory. Even though migration of the extra proton to an amide nitrogen is a prerequisite in the oxazolone mechanism, it was found highly unlikely when this proton was sequestered at an arginine side chain. Possibility of migration of a proton from other locations such as a carboxyl group is discussed.