@article {2649,
	title = {Free Energy Barrier Estimation for the Dissociation of Charged Protein Complexes in the Gas Phase},
	journal = {Journal of Physical Chemistry A},
	volume = {113},
	number = {16},
	year = {2009},
	note = {ISI Document Delivery No.: 435ZUTimes Cited: 4Cited Reference Count: 29Wanasundara, Surajith N. Thachuk, Mark},
	month = {Apr},
	pages = {3814-3821},
	type = {Article},
	abstract = {Free energies are calculated for the protonated cytochrome c{\textquoteright} dimer ion in the gas phase as a function of the center of mass distance between the monomers. A number of different charge partitionings are examined as well as the behavior of the neutral complex. It is found that monomer unfolding competes with complex dissociation and that the relative importance of these two factors depends upon the charge partitioning in the complex. Symmetric charge partitionings preferentially suppress the dissociation barrier relative to unfolding, and complexes tend to dissociate promptly with little structural changes occurring in the monomers. Alternatively, asymmetric charge partitionings preferentially lower the barrier for monomer unfolding relative to the dissociation barrier. In this case, the monomer with the higher charge unfolds before the complex dissociates. For the homodimer considered here, this pathway has a large free energy barrier. The results can be rationalized using schematic two-dimensional free energy surfaces. Additionally, for large multimeric complexes, it is argued that the unfolding and subsequent charging of a single monomer is a favorable process, cooperatively lowering both the unfolding and dissociation barriers at the same time.},
	keywords = {ASSEMBLIES, ELECTROSPRAY-IONIZATION, MASS-SPECTROMETRY, MODEL, MOLECULAR-DYNAMICS, ORIGIN, PATHWAYS, SIMULATIONS, SYSTEMS, THERMAL-DISSOCIATION},
	isbn = {1089-5639},
	url = {<Go to ISI>://000265383200014},
	author = {Wanasundara, S. N. and Thachuk, M.}
}
@article {2231,
	title = {State-of-the-art in atmospheric pressure photoionization for LC/MS},
	journal = {Analytica Chimica Acta},
	volume = {627},
	number = {1},
	year = {2008},
	note = {ISI Document Delivery No.: 358IYTimes Cited: 23Cited Reference Count: 147Robb, Damon B. Blades, Michael W.Sp. Iss. SI},
	month = {Oct},
	pages = {34-49},
	type = {Review},
	abstract = {This review presents our perspective on the state-of-the-art of atmospheric pressure photoionization (APPI) for LC/MS. Its focus is on APPI{\textquoteright}s capabilities and how to utilize them fully. The introduction includes a brief recounting of the history of APPI{\textquoteright}s development, as well as a summary of its operating principles and current position in the field. The primary ionization mechanisms in APPI are then addressed, including direct analyte photoionization (PI), dopant/solvent PI, and thermospray. Next a summary of the ion-molecule reaction pathways available for analyte ionization is presented, along with the conditions required for activating them. APPI{\textquoteright}s performance characteristics are then examined. in effect, this review is an interim report on progress made since Rafaelli and Saba concluded that "The ability... to direct the preferential ion formation towards one particular type...can be extremely useful for qualitative and quantitative determinations. For this purpose, a better insight in the processes involved in the ionization step is strongly needed" [A. Raffaelli, A. Saba, Mass Spectrom. Rev. 22 (2003) 318]. In the conclusion, we focus on areas of APPI technology identified as being either unoptimized or largely unexplored, and having the potential to be improved upon-the crux being that with further research and development improvements in the performance, capabilities, and ease-of-use of APPI may reasonably be anticipated. (C) 2008 Elsevier B.V. All rights reserved.},
	keywords = {ACTIVATED CHEMICAL-IONIZATION, AROMATIC-HYDROCARBONS, atmospheric pressure, BROMINATED FLAME RETARDANTS, CARBON, ELECTROSPRAY-IONIZATION, HUMAN PLASMA, LC-MS/MS, liquid chromatography/mass, LIQUID-CHROMATOGRAPHY, PHOTOIONIZATION, POLYCYCLIC, POROUS GRAPHITIC, PROTON-TRANSFER, review, SPECTROMETRY, TANDEM-MASS-SPECTROMETRY},
	isbn = {0003-2670},
	url = {<Go to ISI>://000259911600004},
	author = {Robb, D. B. and Blades, M. W.}
}
@article {1413,
	title = {Mass spectrometric characterization of lipid-modified peptides for the analysis of acylated proteins},
	journal = {Journal of Mass Spectrometry},
	volume = {41},
	number = {2},
	year = {2006},
	note = {ISI Document Delivery No.: 016BVTimes Cited: 13Cited Reference Count: 45},
	month = {Feb},
	pages = {229-241},
	type = {Article},
	abstract = {The analysis of acylated proteins by mass spectrometry (MS) has largely been overshadowed in proteomics by the analysis of glycosylated and phosphorylated proteins; however, lipid modifications on proteins are proving to be of increasing importance in biomedical research. In order to identify the marker ions and/or neutral loss fragments that are produced upon collision-induced dissociation, providing a means to identify the common lipid modifications on proteins, peptides containing an N-terminally myristoylated glycine, a palmitoylated cysteine and a farnesylated cysteine were chemically synthesized. Matrix-assisted laser desorption/ionization time-of-flight time-of-flight (MALDI-TOF-TOF), electrospray ionization quadrupole time-of-flight (ESI Q-TOF), and electrospray ionization hybrid triple-quadrupole/linear ion trap (ESI QqQ(LIT)) mass spectrometers were used for the analysis. The peptide containing the N-terminally myristoylated glycine, upon CID, produced the characteristic fragments a(1) (240.4 Th) and b(1) (268.4 Th) ions as well as a low-intensity neutral loss of 210 Da (C14H26O). The peptides containing a farnesylated cysteine residue fragmented to produce a marker ion at a m/z of 205 Th (C15H25) as well as other intense farnesyl fragment ions, and a neutral loss of 204 Da (C15H24). The peptides containing a palmitoylated cysteine moiety generated neutral losses of 238 Da (C16H30O) and 272 Da (C16H32OS); however, no marker ions were produced. The neutral losses were more prominent in the MALDI-TOF-TOF spectra, whereas the marker ions were more abundant in the ESI QqQ(LIT) and Q-TOF mass spectra. Copyright (c) 2006 John Wiley \& Sons, Ltd.},
	keywords = {ACID, ELECTROSPRAY-IONIZATION, farnesylation, IMMUNODEFICIENCY-VIRUS TYPE-1, marker ion, MATRIX PROTEIN, MEMBRANE ASSOCIATION, myristoylation, N-MYRISTOYLATION, neutral loss, palmitoylation, PHOSPHORYLATION, POSTTRANSLATIONAL MODIFICATIONS, PRENYLATED, PROTEINS},
	isbn = {1076-5174},
	url = {<Go to ISI>://000235596500011},
	author = {Hoffman, M. D. and Kast, J.}
}
@article {1097,
	title = {Linear ion traps in mass spectrometry},
	journal = {Mass Spectrometry Reviews},
	volume = {24},
	number = {1},
	year = {2005},
	note = {ISI Document Delivery No.: 888OJTimes Cited: 73Cited Reference Count: 145},
	month = {Jan-Feb},
	pages = {1-29},
	type = {Review},
	abstract = {Linear ion traps are finding new applications in many areas of mass spectrometry. In a linear ion trap, ions are confined radially by a two-dimensional (2D) radio frequency (RF) field, and axially by stopping potentials applied to end electrodes. This review focuses on linear ion trap instrumentation. Potentials and ion motion in linear multipole fields and methods of ion trapping, cooling, excitation, and isolation are described. This is followed by a description of various mass discrimination effects that have been reported with linear ion traps. Linear ion traps combined in various ways with three-dimensional (3D) traps, time-of-flight (TOF) mass analyzers, and Fourier transform ion cyclotron resonance mass spectrometers are then given. Linear ion traps can be used as stand alone mass analyzers, and their use for mass analysis by Fourier transforming image currents, by mass selective radial ejection, and by mass selective axial ejection are reviewed. (C) 2004 Wiley Periodicals, Inc.},
	keywords = {analysis, CYCLOTRON-RESONANCE, ELECTROSPRAY-IONIZATION, EXCITATION, EXTERNAL ACCUMULATION, FRINGING FIELDS, INVERSE FOURIER-TRANSFORM, ion traps, linear multipoles, mass, MOLECULE REACTION, OCTOPOLE FIELDS, OF-FLIGHT, QUADRUPOLE, RADIOFREQUENCY, RESONANCE, space charge, STORAGE ASSISTED DISSOCIATION, SYSTEM},
	isbn = {0277-7037},
	url = {<Go to ISI>://000226383800001},
	author = {Douglas, D. J. and Frank, A. J. and Mao, D. M.}
}
@article {827,
	title = {Using ellipsoids to model charge distributions in gas phase protein complex ion dissociation},
	journal = {Canadian Journal of Chemistry-Revue Canadienne De Chimie},
	volume = {82},
	number = {12},
	year = {2004},
	note = {ISI Document Delivery No.: 898JHTimes Cited: 12Cited Reference Count: 31},
	month = {Dec},
	pages = {1736-1744},
	type = {Article},
	abstract = {Gas phase protein complex dissociation was modelled using ellipsoids on which discrete charges were placed in randomly chosen charge sites. A number of sizes, shapes, orientations, and types of ellipsoids were considered. For each case, charge transfer parameters and electrostatic energies were calculated as a function of the fractional surface area. It was found that to within 10-15\%, the charge on product ions after dissociation is distributed according to their fractional surface area. This can imply, for example, that in experiments measuring the dissociation of homodimers, charge asymmetries of greater than 10-15\% in the product ions signal that one of the ions has greatly increased its surface area, such as would occur with unfolding. This assumes that proton transfer occurs on a timescale fast enough that the dissociation products adopt the minimum electrostatic energy configuration. Calculation of this energy shows that it is minimized when one or more of the monomers is in an extended conformation.},
	keywords = {charge asymmetry, CYTOCHROME-C, ELECTROSPRAY-IONIZATION, ellipsoid charge model, EXCHANGE, IONIZATION MASS-SPECTROMETRY, ORIGIN, protein complex dissociation},
	isbn = {0008-4042},
	url = {<Go to ISI>://000227072600011},
	author = {Csiszar, S. and Thachuk, M.}
}
@article {442,
	title = {Tandem mass spectrometry of protein-protein complexes: Cytochrome c-cytochrome b(5)},
	journal = {Journal of the American Society for Mass Spectrometry},
	volume = {13},
	number = {1},
	year = {2002},
	note = {ISI Document Delivery No.: 504QXTimes Cited: 31Cited Reference Count: 53},
	month = {Jan},
	pages = {59-71},
	type = {Article},
	abstract = {An improved method to interpret triple quadrupole MS/MS experiments of complexes of large ions is presented and applied to a study of the complex formed by the proteins cytochrome c and cytochrome b(5). Modeling of the activation and dissociation process shows that most of the reaction occurs near the collision cell exit where ions have the highest internal energies. Experiments at different collision cell pressures or with different collision gases (Ne, Ar, Kr) are interpreted with a previously proposed collision model (Chen et al., Rapid Commun. Mass Spectrom. 1998, 12, 1003-1010) to calculate the internal energy added to ions to cause dissociation. Small but systematic differences under different experimental conditions are attributed to different times available for reaction. A method to correct for this is presented. Ne, Ar, and Kr are found to have similar energy transfer efficiencies. Complexes of cytochrome c and cytochrome b5 are detected in ESI mass spectra but with abundances less than expected from the solution equilibrium. Dissociation of the cytochrome c-cytochrome b(5) complexes with charge k gives as the most abundant fragments, cytochrome b(5)(+3) and cytochrome c(+(k+3)). Adding charges to the complex destabilizes it. A series of cytochrome c variants with Lys residues thought to be involved in solution binding replaced by Ala showed no differences in the energy required to induce dissociation of the gas phase complex. The implications for the binding of the gas phase ions are inconclusive. (J Am Soc Mass Spectrom 2002, 13, 59-71) ((C)) 2002 American Society for Mass Spectrometry.},
	keywords = {ACTIVATION, BINDING, COLLISION-INDUCED DISSOCIATION, CROSS-SECTIONS, ELECTROSPRAY-IONIZATION, GAS-PHASE, INTERNAL ENERGY, ION-TRAP, NONCOVALENT COMPLEXES, YEAST ISO-1-FERRICYTOCHROME-C},
	isbn = {1044-0305},
	url = {<Go to ISI>://000172868300007},
	author = {Mauk, M. R. and Mauk, A. G. and Chen, Y. L. and Douglas, D. J.}
}
@article {5189,
	title = {Collision-induced dissociation of bradykinin ions in the interface region of an ESI-MS},
	journal = {Journal of the American Society for Mass Spectrometry},
	volume = {12},
	number = {7},
	year = {2001},
	note = {ISI Document Delivery No.: 447HHTimes Cited: 17Cited Reference Count: 42},
	month = {Jul},
	pages = {772-779},
	type = {Article},
	abstract = {By applying different electric field strengths to the orifice-skimmer region of an electrospray ionization mass spectrometer, the rate of dissociation can be varied based on the amount of infernal energy acquired by an ion through collisions: with the curtain gas molecules. Both the Arrhenius equation and Rice-Ramsperger-Kassel (RRK) theory can be used to predict the rate of dissociation of internally excited molecules. A previously determined model for collision-induced dissociation is tested by comparison of predicted and experimentally observed orifice-skimmer potential differences for dissociation of ions. The rate of collision-induced dissociation of bradykinin ions is determined by monitoring the fragments produced in a mass spectrometer. The semi-quantitative model is found to yield effective predictions when accurate Arrhenius and RRK parameters are utilized. (C) 2001 American Society for Mass Spectrometry.},
	keywords = {ACTIVATION, CYTOCHROME-C, ELECTROSPRAY-IONIZATION, GAS-PHASE, IDENTIFICATION, INFRARED RADIATIVE DISSOCIATION, IONIZATION MASS-SPECTROMETRY, MOLECULES, PEPTIDES, PROTEIN IONS},
	isbn = {1044-0305},
	url = {<Go to ISI>://000169565500002},
	author = {Schneider, B. B. and Douglas, D. J. and Chen, D. D. Y.}
}
@article {4726,
	title = {Methanol-induced conformations of myoglobin at pH 4.0},
	journal = {Biochemistry},
	volume = {39},
	number = {47},
	year = {2000},
	note = {ISI Document Delivery No.: 378UETimes Cited: 62Cited Reference Count: 78},
	month = {Nov},
	pages = {14702-14710},
	type = {Article},
	abstract = {The equilibrium methanol-induced conformation changes of holomyoglobin (hMb) at pH 4.0 have been studied by circular dichroism, tryptophan fluorescence, and Soret band absorption and by electrospray ionization mass spectrometry (ESI-MS). Optical spectra show the following: (1) In 35-40\% (v/v) methanol/water, the native-like secondary structure remains, the tertiary structure is lost, the heme protein interactions are decreased, and a folding intermediate is formed. (2) In 50\% methanol, heme is lost from the protein, and there is a small decrease in helicity together with a loss of tertiary structure. (3) At > 60\% methanol, the helicity increases and the apoprotein goes into a helical denatured state. The conformations are also probed by the charge states produced in ESI-MS and by hydrogen/deuterium (H/D) exchange with mass measurement by ESI-MS. At 0-30\% methanol, native hMb produces relatively low charge states (9(+)-13(+)) in ESI-MS and exchanges relatively few hydrogens. In 35-40\% methanol, at which an intermediate is formed, there is a bimodal distribution of hMb ions with both low (9(+)-13(+)) and high (14(+)-23(+)) charge states and also a high charge state distribution (12(+)-26(+)) of apomyoglobin (aMb) ions. Low and high charge states of hMb and a high charge state of aMb all show the same H/D exchange rate, indicating that an unfolded hMb intermediate interconverts between folded hMb and unfolded aMb. The charge state distribution for the unfolded hMb intermediate observed here is similar to that of the recently reported transient intermediate formed during the acid denaturation of hMb. At 50\% alcohol the protein produces predominantly high charge states of aMb ions and shows H/D exchange rates close to those of the acid-denatured protein. H/D exchange of the helical denatured protein at alcohol concentrations >60\%, at which high charge states of aMb are produced, shows that the protein structure is more protected than at similar to 50\% methanol.},
	keywords = {AMIDE HYDROGEN-EXCHANGE, APOMYOGLOBIN, BETA-LACTOGLOBULIN, CYTOCHROME-C, ELECTROSPRAY-IONIZATION, FOLDING INTERMEDIATE, IONIZATION MASS-SPECTROMETRY, MOLTEN GLOBULE INTERMEDIATE, SPERM-WHALE, STRUCTURAL-CHARACTERIZATION, X-RAY-SCATTERING},
	isbn = {0006-2960},
	url = {<Go to ISI>://000165602400040},
	author = {Babu, K. R. and Douglas, D. J.}
}
@article {4222,
	title = {A new linear ion trap time-of-flight system with tandem mass spectrometry capabilities},
	journal = {Rapid Communications in Mass Spectrometry},
	volume = {12},
	number = {20},
	year = {1998},
	note = {ISI Document Delivery No.: 130DBTimes Cited: 92Cited Reference Count: 64},
	pages = {1463-1474},
	type = {Article},
	abstract = {A new hybrid linear ion trap time-of-flight mass spectrometer has been constructed and the first results for tandem-in-time MS/MS in a 2-dimensional Paul trap are presented. The instrument consists of an electrospray ionization source and two radio frequency (RF) only quadrupoles operating at a pressure of 7 mTorr N-2 which are coupled orthogonally to a linear TOFMS. Ions are trapped in an RF-only quadrupole through the application of timed stopping potentials on the entrance and exit apertures. Through the coupling of an auxiliary waveform generator on one pair of the ion trap rods a small dipolar excitation voltage is superimposed on the quadrupolar electric field. This voltage is used for precursor isolation via broadband excitation and collision induced dissociation through mass selective resonant excitation. Instrumental performance and choice of operating parameters are demonstrated by recording fragment spectra for +3 ions of renin substrate and fl ions of reserpine. TOFMS mass resolution (m/Delta m)(FWHM) is as high as 740 at m/z = 609. Fragmentation efficiency is greater than 50\% and excitation mass resolution is 60-75. (C) 1998 John Wiley \& Sons, Ltd.},
	keywords = {DECOMPOSITION, EJECTION, ELECTROSPRAY-IONIZATION, FREQUENCY STANDARD APPLICATIONS, MOLECULE REACTION, PARAMETERS, PERFORMANCE, PROTEINS, QUADRUPOLE, RESONANCE, SPECTROSCOPY},
	isbn = {0951-4198},
	url = {<Go to ISI>://000076503200007},
	author = {Campbell, J. M. and Collings, B. A. and Douglas, D. J.}
}
@article {4227,
	title = {Stability of a highly charged noncovalent complex in the gas phase: Holomyoglobin},
	journal = {Rapid Communications in Mass Spectrometry},
	volume = {12},
	number = {15},
	year = {1998},
	note = {ISI Document Delivery No.: 105GATimes Cited: 33Cited Reference Count: 56},
	pages = {1003-1010},
	type = {Article},
	abstract = {Gas phase holomyoglobin (hMb) ions in charge states +7 to +21 were formed by electrospray ionization in combination with a continuous-flow mixing apparatus. Collision cross section measurements show that the highly charged ions are somewhat unfolded in comparison to low charge states but still retain a considerable degree of folding. A new collision model is presented which calculates the relative energies transferred to complexes in tandem mass spectrometry. Tandem mass spectrometry and ion trapping experiments both show that the energies required to dissociate heme from the highly charged heme-protein complexes in the gas phase are similar to those of low charge states, previously shown in literature ion cyclotron resonance experiments to be 0.7-1.0 eV, These energies are comparable to those of the heme binding energy in solution. The results suggest that even for the highly charged hMb ions which have unfolded somewhat, the heme-protein interactions remain relatively unperturbed. (C) 1998 John Wiley \& Sons, Ltd.},
	keywords = {CONFORMATION, CYTOCHROME-C, ELECTROSPRAY-IONIZATION, ion-molecule, IONIZATION MASS-SPECTROMETRY, METMYOGLOBIN, MYOGLOBIN, PROTEIN IONS, PROTON-TRANSFER REACTIVITY, QUADRUPOLE, reaction},
	isbn = {0951-4198},
	url = {<Go to ISI>://000075063300003},
	author = {Chen, Y. L. and Campbell, J. M. and Collings, B. A. and Konermann, L. and Douglas, D. J.}
}
