Surface induced dissociation of chromium hexacarbonyl on fluorinated alkanethiolate surface in ion cyclotron resonance mass spectrometer: studies of energetics of the process using recursive internal energy distribution search method

Rakov, V. Sergey; Denisov, Eduard; Ridge, D. P.

doi:10.1016/s1387-3806(01)00505-x

Cited by 13 publications

(17 citation statements)

References 30 publications

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“…Sample solutions were infused into the ESI source using a Harvard Apparatus (Natick, MA) syringe pump at a flow rate of 10 to 50 L/h. Detailed description of the experimental setup for SID experiments can be found in published work [32] and has been used for the study of related polyalanine peptides [33,34]. Briefly, the surface was introduced into the ICR cell through the aperture in the rear ICR trapping plate at 90°to the magnetic field.…”

Section: Sid Experimentsmentioning

confidence: 99%

Evaluation of the influence of amino acid composition on the propensity for collision-induced dissociation of model peptides using molecular dynamics simulations

Cannon

Taasevigen

Baxter

et al. 2007

J. Am. Soc. Mass Spectrom.

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The dynamical behavior of model peptides was evaluated with respect to their ability to form internal proton donor-acceptor pairs using molecular dynamics simulations. The proton donor-acceptor pairs are postulated to be prerequisites for peptide bond cleavage resulting in formation of b and y ions during low-energy collision-induced dissociation in tandem mass spectrometry (MS/MS). The simulations for the polyalanine pentamer Ala(5)H(+) were compared with experimental data from energy-resolved surface induced dissociation (SID) studies. The results of the simulation are insightful into the events that likely lead up to the fragmentation of peptides. Nine-mer polyalanine-based model peptides were used to examine the dynamical effect of each of the 20 common amino acids on the probability to form donor-acceptor pairs at labile peptide bonds. A range of probabilities was observed as a function of the substituted amino acid. However, the location of the peptide bond involved in the donor-acceptor pair plays a critical role in the dynamical behavior. This influence of position on the probability of forming a donor-acceptor pair would be hard to predict from statistical analyses on experimental spectra of aggregate, diverse peptides. In addition, the inclusion of basic side chains in the model peptides alters the probability of forming donor-acceptor pairs across the entire backbone. In this case, there are still more ionizing protons than basic residues, but the side chains of the basic amino acids form stable hydrogen bond networks with the peptide carbonyl oxygens and thus act to prevent free access of "mobile protons" to labile peptide bonds. It is clear from the work that the identification of peptides from low-energy CID using automated computational methods should consider the location of the fragmenting bond as well as the amino acid composition.

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Section: Sid Experimentsmentioning

confidence: 99%

Evaluation of the influence of amino acid composition on the propensity for collision-induced dissociation of model peptides using molecular dynamics simulations

Cannon

Taasevigen

Baxter

et al. 2007

J. Am. Soc. Mass Spectrom.

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“…A main method deconvolutes the fragmentation graphs of thermometer molecules, usually from photoelectron-photoion coincidence (PEPICO) measurements, and compares these with fragmentation following CID or SID activation to assign the internal energies of the collisionally activated ions. Ferrocene and metal carbonyl ions that lose (CO) ligands stepwise were applied as thermometer molecules [9,[38][39][40][41]. The drawbacks are that not many breakdown graphs are available, and the breakdown graphs are affected by instrument-dependent kinetic shifts.…”

Section: Thermal Extrapolation For Ion Thermometry and Comparison Wimentioning

confidence: 99%

A thermal extrapolation method for the effective temperatures and internal energies of activated ions

Meot‐Ner¹,

Somogyi²

2007

International Journal of Mass Spectrometry

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“…On colliding with a neutral gas molecule, some of the kinetic energy can be converted into internal energy. The internal energy deposition function (EDF) during the collisional activation has been investigated in several studies including the "thermometer" ion method by Cooks and co-workers [25], the "deconvolution" method by Vekey [26,27], the recursive internal energy distribution search (RIEDS) method by Futrell [28], the probability theoretical method [29,30], and several other theoretical studies of the efficiency of the energy transfer on collisional activation [31,32]. The effects of size and structure of the peptide, mass of the collisional activator, and the collisional energy have been addressed in these studies.…”

Section: Internal Energy Considerationsmentioning

confidence: 99%

A mini-review of mass spectrometry using high-performance FTICR-MS methods

Heeren

Kleinnijenhuis

McDonnell

et al. 2004

Analytical and Bioanalytical Chemistry

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Structural characterization of macromolecules is currently delivering new insights into the behavior of individual molecules or molecular ensembles. Technological advances have made it possible to examine smaller and smaller amounts (down to single molecules) of larger and larger molecular systems. Mass spectrometry in particular is capable of the detailed study of extremely small quantities (down to a single molecule) of very large (biological) molecules. The advent of new ionization techniques such as electrospray and matrix-assisted laser desorption are mainly responsible for these advances. As a result, mass spectrometry has evolved into an enabling discipline that plays an increasingly important role in combinatorial chemistry, polymer science, biochemistry, medicine, environmental and marine science, and archaeology and conservation science. This paper will review a selection of methodological developments in the field of high-performance Fourier transform ion cyclotron resonance mass spectrometry for structural analysis of these macromolecules.

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Surface induced dissociation of chromium hexacarbonyl on fluorinated alkanethiolate surface in ion cyclotron resonance mass spectrometer: studies of energetics of the process using recursive internal energy distribution search method

Cited by 13 publications

References 30 publications

Evaluation of the influence of amino acid composition on the propensity for collision-induced dissociation of model peptides using molecular dynamics simulations

Evaluation of the influence of amino acid composition on the propensity for collision-induced dissociation of model peptides using molecular dynamics simulations

A thermal extrapolation method for the effective temperatures and internal energies of activated ions

A mini-review of mass spectrometry using high-performance FTICR-MS methods

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