Classical trajectories and RRKM modeling of collisional excitation and dissociation of benzylammonium and tert-butyl benzylammonium ions in a quadrupole-hexapole-quadrupole tandem mass spectrometer

Abstract

Collision-induced dissociation of the benzylammonium and the 4-tert-butyl benzylammonium ions was studied experimentally in an electrospray ionization quadrupole-hexapole-quadrupole tandem mass spectrometer. Ion fragmentation efficiencies were determined as functions of the kinetic energy of ions and the collider gas (argon) pressure. A theoretical Monte Carlo model of ion collisional excitation, scattering, and decomposition was developed. The model includes simulation of the trajectories of the parent and the product ions flight through the hexapole collision cell, quasiclassical trajectory modeling of collisional activation and scattering of ions, and Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the parent ion decomposition. The results of modeling demonstrate a general agreement between calculations and experiment. Calculated values of ion fragmentation efficiency are sensitive to initial vibrational excitation of ions, scattering of product ions from the collision cell, and distribution of initial ion velocities orthogonal to the axis of the collision cell. Three critical parameters of the model were adjusted to reproduce the experimental data on the dissociation of the benzylammonium ion: reaction enthalpy and initial internal and translational temperatures of the ions. Subsequent application of the model to decomposition of the t-butyl benzylammonium ion required adjustment of the internal ion temperature only. Energy distribution functions obtained in modeling depend on the average numbers of collisions between the ion and the atoms of the collider gas and, in general, have non-Boltzmann shapes. (J Am Soc Mass Spectrom 2010, 21, 425-439) © 2010 American Society for Mass Spectrometry F ragmentation of gaseous ions has long been an important source of information on the properties of these ions and the corresponding parent species. Studies of collision-induced dissociation (CID) mass spectra of many types of ions provide important information on their structure, thermochemistry, and other properties; recently, the main focus of such studies shifted to the analysis of large biomolecules, such as proteins and peptides (e.g., [1][2][3][4][5][6][7][8][9][10][11].As a result of many studies, the many features of collisional ion dissociation have been elucidated, including those of fragmentation of the ions of large biomolecules (e.g., [9,[12][13][14][15][16][17] and references therein). However, the factors that determine absolute and relative abundances of possible fragments are not well understood, certainly not to the point that would enable quantitative prediction of CID mass spectra. It is generally understood that the successful modeling of collisional ion dissociation would require correct quantitative description of three factors: (1) the chemical mechanism of fragmentation (i.e., the sequence of intramolecular rearrangements and decomposition and the potential energy surfaces of these processes), (2) rovibrational excitation of the parent ion as a result of collisions with the inert collider gas, a...

Using dissociation energies to predict observability of b‐ and y‐peaks in mass spectra of short peptides. II. Results for hexapeptides with non‐polar side chains

“…[22] We attribute this discrepancy mainly to the importance of entropy contributions which are completely neglected in Eqn. (3). There also might be a number of other factors influencing the observed intensities.…”

“…[1] Moreover, accurate predictions of ion intensity relationships would also require detailed knowledge of experimental conditions (which is not always available) and also a satisfactory theoretical description of other physical processes (collisional heating, electronic excitations, thermalization, etc.). [2][3][4][5][6][7] Although accurate prediction of relative ion intensities remains a task for the future, we believe that one already can take advantage of the achieved understanding [8][9][10][11][12][13][14][15][16][17][18][19][20][21] of peptide fragmentation mechanisms. A practical way to do so would be to introduce a filtering of the theoretical peaks of candidate peptides before scoring their similarity with the given experimental spectrum.…”

Correction of precursor and product ion relative abundances in order to standardize CID spectra and improve Ecom50 accuracy for non-targeted metabolomics

“…Theoretical models developed by Knyazev and Stein (Knyazev & Stein 2010) suggest that product ions may have lower absolute ion transfer efficiencies as compared to precursor ions of similar m/z due to additional kinetic energy acquired during CID. The calculated precursor ion efficiency was not included in their results, thus the magnitude of this difference could not be ascertained.…”

Selective collision‐induced fragmentation of ortho‐hydroxybenzyl‐aminated lysyl‐containing tryptic peptides

“…2(A) for the doubly charged precursor ion, the triply charged precursor ion also produces a doubly charged product ion of m/z 341. 21 21 and 227.81 correspond to the calculated unmodified m/z ratios for the peptide HAKLGR as doubly and triply charged peptides, respectively. This suggests that the lysyl residue adopts its normal primary e-amino structure after cleavage of the C z -N e bond from both fragmentation mechanisms and this was confirmed via the acquisition LGR; however, one slight difference to emphasize is that there is evidence that the CCE pathway is an active fragmentation channel for the doubly charged precursor of IGK o-OH GVAR represented by the peak at m/z 700.45 in Fig.…”