@article {2402,
	title = {LINEAR QUADRUPOLES IN MASS SPECTROMETRY},
	journal = {Mass Spectrometry Reviews},
	volume = {28},
	number = {6},
	year = {2009},
	note = {ISI Document Delivery No.: 515CWTimes Cited: 5Cited Reference Count: 145Douglas, D. J.},
	month = {Nov-Dec},
	pages = {937-960},
	type = {Review},
	abstract = {The use of linear quadrupoles in mass spectrometry as mass filters and ion guides is reviewed. Following a tutorial review of the principles of mass filter operation, methods of mass analysis are reviewed. Discussed are extensions of quadrupole mass filters to higher masses, scanning with frequency sweeps of the quadrupole waveform, operation in higher stability regions, and operation with rectangular or other periodic waveforms. Two relatively new methods of mass analysis the use of "islands of stability" and "mass selective axial ejection" are then reviewed. The optimal electrode geometry for a quadrupole mass filter constructed with round rods is discussed. The use of collisional cooling in quadrupole ion guides is discussed along with ion guides that have axial fields. Finally, mass analysis with quadrupoles that have large distortions to the geometry and fields is discussed. An Appendix gives a brief tutorial review of definitions of electrical potentials and fields, as well as the units used in this article. (C) 2009 Wiley Periodicals, Inc., Mass Spec Rev 28:937-960, 2009},
	keywords = {2ND STABILITY REGION, axial fields, AXIAL-FIELD, CHARGED-PARTICLE, COLLISION-INDUCED DISSOCIATION, distorted fields, FRINGING FIELDS, ion guide, ION OPTICAL-PROPERTIES, linear, mass filter, mass scans, multipoles, OCTOPOLE FIELDS, QUADRUPOLE, quadrupole excitation, RADIO-FREQUENCY, RESOLUTION, SEPARATION MODE, STABILITY, TRAJECTORIES, VOLTAGE COMPONENT},
	isbn = {0277-7037},
	url = {<Go to ISI>://000271445200005},
	author = {Douglas, D. J.}
}
@article {2175,
	title = {Gas-phase proton-transfer pathways in protonated histidylglycine},
	journal = {Rapid Communications in Mass Spectrometry},
	volume = {22},
	number = {18},
	year = {2008},
	note = {ISI Document Delivery No.: 355WATimes Cited: 2Cited Reference Count: 23MacDonald, Brandon I. Thachuk, Mark},
	month = {Sep},
	pages = {2946-2954},
	type = {Article},
	abstract = {Pathways for proton transfer in the histidylglycine cation are examined in the gas-phase environment with the goal of understanding the mechanism by which protons may become mobile in proteins with basic amino acid residues. An extensive search of the potential energy surface is performed using density functional theory (DFT) methods. After corrections for zero-point energy are included, it is found that all the lowest energy barriers for proton transfer between the N-terminus and the imidazole ring have heights of only a few kcal/mol, while those between the imidazole ring and the backbone amide oxygen have heights of approximately 15 kcal/mol when the proton is moving from the ring to the backbone and only a few kcal/mol when moving from the backbone to the imidazole ring. In mass spectrometric techniques employing collision-induced dissociation to dissociate protein complex ions or to fragment peptides, these barriers can be overcome, and the protons mobilized. Copyright (C) 2008 John Wiley \& Sons, Ltd.},
	keywords = {COLLISION-INDUCED DISSOCIATION, fragmentation, IONIZATION, MASS-SPECTROMETRY, mobility, MODEL, ORIGIN, PEPTIDE IONS},
	isbn = {0951-4198},
	url = {<Go to ISI>://000259738700023},
	author = {MacDonald, B. I. and Thachuk, M.}
}
@article {1414,
	title = {Multiple neutral loss monitoring (MNM): A multiplexed method for post-translational modification screening},
	journal = {Journal of the American Society for Mass Spectrometry},
	volume = {17},
	number = {3},
	year = {2006},
	note = {ISI Document Delivery No.: 021SETimes Cited: 11Cited Reference Count: 20},
	month = {Mar},
	pages = {307-317},
	type = {Article},
	abstract = {Post-translational modifications of proteins are involved in determining the activity of proteins and are essential for proper protein function. Current mass spectrometric strategies require one to specify a particular type of modification, in some cases also a particular charge state of a protein or peptide that is to be studied before the actual analysis. Due to these requirements, most of the modifications on proteins are not considered in such an experiment and, thus, a series of similar analyses need to be performed to ensure a more extensive characterization. A novel scan strategy has been developed, multiple neutral loss monitoring (MNM), allowing for the comprehensive screening of post-translational modifications (PTM) on proteins that fragment as neutral losses in a mass spectrometer. MNM method parameters were determined by performing product ion scans on a number of modified peptides over a range of collision energies, providing neutral loss energy profiles and optimal collision energies (OCE) for each modification, supplying valuable information pertaining to the fragmentation of these modifications and the necessary parameters that would be required to obtain the best analysis. As the optimal collision energy was highly dependent on the type of modification and the charge state of the peptide, the MNM scan was operated with a collision energy gradient. Autocorrelation analyses identified the type of modification, and convolution mapping analyses identified the associated peptide. The MNM scan with the new collision energy parameters was successfully applied to a mixture of four modified peptides in a BSA digest. The implementation of this technique will allow for comprehensive screening of all modifications that fragment as neutral losses.},
	keywords = {COLLISION-INDUCED DISSOCIATION, PEPTIDES, PROTEIN-PHOSPHORYLATION, PROTEOMIC ANALYSIS, SCAN, TANDEM MASS-SPECTROMETRY},
	isbn = {1044-0305},
	url = {<Go to ISI>://000236004700004},
	author = {Hoffman, M. D. and Sniatynski, M. J. and Rogalski, J. C. and Le Blanc, J. C. Y. and Kast, J.}
}
@article {1238,
	title = {Statistical evaluation of electrospray tandem mass spectra for optimized peptide fragmentation},
	journal = {Journal of the American Society for Mass Spectrometry},
	volume = {16},
	number = {4},
	year = {2005},
	note = {ISI Document Delivery No.: 911RDTimes Cited: 6Cited Reference Count: 33},
	month = {Apr},
	pages = {505-514},
	type = {Article},
	abstract = {Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has become the method of choice for the analysis of complex peptide mixtures. It combines the separation power of nanoflow LC with highly specific sequence analysis, allowing automated peptide sequencing with high resolution and throughput. For peptide fragmentation, the current experimental setup uses predefined parameters based on the mass-to-charge ratio of the individual precursor. Suitable parameters are typically established by empirical evaluation of fragment spectra of individual peptides used as standards. As a result, nonoptimal fragment spectra are obtained if peptides show fragmentation behavior different from these standards, which often result in the loss of sequence-specific fragment ion information. Here we describe a statistical approach for the systematic evaluation of the quality of individual peptide fragment spectra based on the calculation of their arithmetic mean and standard deviation. The method utilizes the dependence of these parameters on the difference in electric potential across the collision cell to determine the value that results in maximum information content. We show that the method is applicable to fragment spectra generated from a variety of multiply-charged tryptic peptides, over a wide concentration range, and on different types of mass analyzers. We also show how this novel approach can be used to define optimized collision energy settings over a wide mass-to-charge range. (J Am Soc Mass Spectrom 2005,16,505-514) (c) 2005 American Society for Mass Spectrometry},
	keywords = {ALGORITHM, ASSISTED-LASER-DESORPTION/IONIZATION, COLLISION-INDUCED DISSOCIATION, DATABASE SEARCH, MIXTURES, PROTEIN IDENTIFICATION, PROTEOMICS, PROTONATED PEPTIDES, SPECTROMETRY},
	isbn = {1044-0305},
	url = {<Go to ISI>://000228021400010},
	author = {Rogalski, J. C. and Lin, M. S. and Sniatynski, M. J. and Taylor, R. J. and Youhnovski, N. and Przybylski, M. and Kast, J.}
}
@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.}
}
