N-Acylated Dipeptide Tags Enable Precise Measurement of Ion Temperature in Peptide Fragmentation

Multi-functional MBIT for peptide tandem mass spectrometry

Isobaric tags have been widely used for the identification and quantification of proteins in mass spectrometry-based proteomics. The mass-balanced, (1) H/(2) H isotope-coded dipeptide tag (MBIT) is a multifunctional isobaric tag based on N-acetyl-Ala-Ala dipeptide containing an amine-reactive linker that conjugates the tag to the primary amines of proteolytic peptides. MBITs provide a pair of isotope-coded quantitation signals separated by 3 Da, which enables 2-plex quantification and identification of proteins in the 15-250 fmol range. Various MBITs diversified at the N-acetyl group or at the side chain of the first alanine provide a pair of bs ions as low-mass quantitation signals in a distinct mass window. Thus, a combination of different MBITs allows multiplex quantification of proteins in a single liquid chromatography-mass spectrometry experiment. Unlike other isobaric tags, MBITs also offer a pair of ys ions as high-mass quantitation signals in a noise-free region, facilitating protein quantification in quadrupole ion trap mass spectrometers. Uniquely, bS ions, forming N-protonated oxazolone, undergo unimolecular dissociation and generate the secondary low-mass quantitation signals, aS ions. The yield of aS ions derived from bS ions can be used to measure the temperature of bS ions, which enables a reproducible acquisition of the peptide tandem mass spectra. Thus, MBITs enable multiplexed quantitation of proteins and the concurrent measurement of ion temperature using bS and aS signal ions as well as the isobaric protein quantitation in resonance-type ion trap using yS (complement of bS ) signal ions. This review provides an overview of MBITs with a focus on the multi-functionality that has been successfully demonstrated in the peptide tandem mass spectrometry.

Coupled unimolecular dissociation kinetics of bromotoluene radical cations

The unimolecular dissociations of o-, m-, and p-bromotoluene radical cations to C7H7(+) (benzylium and tropylium) are examined by considering the coupling of the three isomers in the dissociation pathways. The potential energy surface obtained from ab initio calculations suggests the interconversion of isomers through methylene and hydrogen migrations on the ring. The rate equations for each isomer are combined together to form a rate matrix for coupled reactions. The rate matrix contains the microcanonical rate constants for all elementary steps, which are calculated using Rice-Ramsperger-Kassel-Marcus theory based on the molecular parameters obtained from density functional theory. The unimolecular dissociation rates for coupled reactions are determined by numerically solving the matrix equation. As a result of reaction coupling, the product branching ratio becomes time-dependent and the reaction rates of three isomers become parallel to one another as the energy increases, although their initial rates differently vary with energy. The calculated rate-energy curves fall below the time-resolved photodissociation data in the energy range 2.2-2.7 eV but are in line with the photoelectron photoion coincidence data in the energy range 2.7-3.5 eV. The discrepancy between experiment and theory in the low-energy region is ascribed to the uncertainties of the potential energy surface as well as the contribution of the radiative relaxation rate that has not been taken into account in the theoretical calculations. The rate-energy curves are then used to calculate the thermal reaction rate constants, and the Arrhenius parameters are determined in the temperature range 700-1300 K. Comparison of the activation energy and entropy obtained from the Arrhenius plot with the calculated enthalpy and entropy changes between the reactant and the highest-lying transition state suggests that a series of [1,2] H-atom migrations occurring near the entrance comprise the rate-determining steps and the subsequent [1,2] H-atom migrations play an important role in increasing the activation energy and decreasing the entropy by reducing the net flux to the exit.