Call number: LD2668 .T4 1979 T85 / Master of Science

published_or_final_version / abstract / Physics / Doctoral / Doctor of Philosophy

As an additional study, effect of tyrosine nitration on the BCD of protonated and metalated peptides was investigated. Some fragment ions that were inhibited in the ECD of protonated peptides were liberated in the ECD of metalated peptides. By theoretical calculation of the cation-pi and cation-nitro group coordination using the metal ions nitrated phenol complex as a model, it is found that the metal ions might favor coordinating with the nitro group of the nitrated tyrosine residue in the peptides. / In order to improve the performance of the electron capture dissociation (BCD) mass spectrometry for structural analysis of peptides/proteins, BCD of peptides cationized with various transition metal ions was investigated. It was found that peptides adducted with different divalent transition metal ions generated different BCD tandem mass spectra. For Mn2+and Zn2+, the incoming low-energy electron would not favor being trapped by the metal ions and instead trigger the usual BCD dissociation channel(s) via "hot-hydrogen" or "superbase" intermediates to form a series of c-/z·- fragments. For other first row transition metal ions, including Fe2+, Co2+, Ni 2+and Cu2+, reduction of the metal ions occurs preferentially during the electron capture event and lead to the formation of usual "slow-heating" type of fragment ions, i.e. metalated a-/y-fragments & metalated b-/y- fragments. / To further compare the behavior of metal ions with the same electronic configuration, BCD of Group IIB metal ions adducted peptides were investigated. In contrast to the ECD behavior of Zn2+ adducted peptides, peptide radical cations (M+· ) and fragment ions corresponding to losses of neutral side chain from M+· were observed in the ECD spectra of Hg2+ and Cd2+ adducted peptides. The experimental observations appeared to depend on the balance of the ionization energy of peptide and the solvation modulated ionization energies of the metal atom. The reduction of divalent metal ions by the electron capture event could induce spontaneous electron transfer from the peptide moiety to the monovalent metal centre and generate hydrogen-deficient M +· species. / Chen, Xiangfeng. / Adviser: T.-W. Dominic Chan. / Source: Dissertation Abstracts International, Volume: 73-06, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 131-139). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

by Siu-Chung Wong. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1988. / Bibliography: leaves 98-102.

Chen, Fan. / "October 2010." / Thesis (M.Phil.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 85-91). / Abstracts in English and Chinese. / ABSTRACT --- p.III / 摘要 --- p.IV / ACKNOWLEDGENTS --- p.V / TABLE OF CONTENTS --- p.VI / LIST OF FIGURES --- p.VIII / LIST OF TABLES --- p.X / SYMBOLS AND ABBREVIATIONS --- p.XI / Chapter CHAPTER 1 --- INTRODUCTION --- p.1 / Chapter 1.1 --- Mass spectrometry in proteomics --- p.1 / Chapter 1.2 --- Fourier-transform ion cyclotron resonance mass spectrometry --- p.2 / Chapter 1.2.1 --- Introduction --- p.2 / Chapter 1.2.2 --- Ionization --- p.3 / Chapter 1.2.3 --- Ions in ICR --- p.4 / Chapter 1.2.4 --- Ions excitation and detection --- p.7 / Chapter 1.3 --- Tandem mass spectrometry --- p.8 / Chapter 1.4 --- Electron capture dissociation --- p.12 / Chapter 1.4.1 --- Features ofECD --- p.13 / Chapter 1.4.2 --- Two popular mechanisms for ECD --- p.14 / Chapter 1.4.2.1 --- The Cornell mechanism --- p.15 / Chapter 1.4.2.2 --- The Utah-Washington mechanism --- p.17 / Chapter 1.4.3 --- Recombination energy --- p.19 / Chapter 1.5 --- Outline of the present work --- p.21 / Chapter CHAPTER 2 --- INSTRUMENTATION AND EXPERIMENTAL --- p.22 / Chapter 2.1 --- Fourier-transform ion cyclotron resonance mass spectrometer --- p.22 / Chapter 2.1.1 --- Vacuum system --- p.24 / Chapter 2.1.2 --- Nanospray system --- p.26 / Chapter 2.1.3 --- Ion transfer system --- p.29 / Chapter 2.1.4 --- Infinity´ёØ cell --- p.29 / Chapter 2.1.5 --- Electron emission source --- p.31 / Chapter 2.1.6 --- Data acquisition system --- p.32 / Chapter 2.2 --- Experimental --- p.32 / Chapter 2.2.1 --- Simple ESI acquisition pulse program --- p.32 / Chapter 2.2.2 --- ESI-ECD acquisition pulse program --- p.35 / Chapter CHAPTER 3 --- FRAGMENTATION OF MODEL PEPTIDE IONS IN DIFFERENT CHARGE STATES UNDER ECD CONDITIONS --- p.38 / Chapter 3.1 --- Introduction --- p.38 / Chapter 3.2. --- Experimental --- p.41 / Chapter 3.2.1 --- Sequence design and sample preparation --- p.41 / Chapter 3.2.2 --- ECD under fourier-transform ion cyclotron mass spectrometer --- p.43 / Chapter 3.3 --- Results and discussion --- p.43 / Chapter 3.3.1 --- General features of ECD spectra --- p.43 / Chapter 3.3.1.1 --- ECD of RRRR --- p.43 / Chapter 3.3.1.2 --- ECD of KKKK --- p.47 / Chapter 3.3.2 --- Effect of charge state of precursor ions --- p.49 / Chapter 3.3.3 --- Effect of proton carriers --- p.52 / Chapter 3.3.4 --- Effect of proton carrier location --- p.54 / Chapter 3.4 --- Conclusions --- p.60 / Chapter CHAPTER 4 --- EFFECT OF PRECURSOR ION HETEROGENEITY ON ECD FRAGMENTATION --- p.62 / Chapter 4.1 --- Introduction --- p.62 / Chapter 4.2 --- Method --- p.63 / Chapter 4.2.1 --- Preferential dissociation index --- p.64 / Chapter 4.2.2 --- Precursor ion heterogeneity --- p.65 / Chapter 4.3 --- Results and discussion --- p.67 / Chapter 4.3.1 --- PDI in model peptides --- p.67 / Chapter 4.3.2 --- PIH and PDI in RRRR and KKKK --- p.71 / Chapter 4.3.3 --- PDI and PIH in two-lysine containing peptides --- p.73 / Chapter 4.3.4 --- PDI and PIH in other peptides --- p.80 / Chapter 4.4 --- Conclusions --- p.82 / Chapter CHAPTER 5 --- CONCLUSIONS --- p.83 / References --- p.85 / Chapter Appendix I: --- Pulse program for simple MS and MS/MS experiment --- p.92 / Chapter (A) --- Simple ESI FT-ICR MS experiment --- p.92 / Chapter (B) --- ESI ECD FT-ICR MS experiment --- p.95 / Chapter Appendix II: --- ECD spectra of AC-XAAAXAAAXAAAX-NH2 peptide series in different charge states --- p.99 / Chapter Appendix III: --- The PDI of the hypothetic peptide --- p.110 / Chapter Appendix IV: --- The PIH among the investigated system --- p.111

Protons with energies ranging from 0.4 to 2.0 MeV were used to measure K-shell vacancy production cross sections (oVK) for N_2, CH_4, C_2H_4, C_2H_6, and CO_2 gas targets under single collision conditions. An electron-ion time-of-flight coincidence technique was used to determind the ration of the K-K electron capture cross section, OECK, to the K-vacancy production cross section, oVK. These ratios were then combined with the measured values of oVK to extract the K-K electron capture cross sections. Measurements were also made for protons of the same energy range but with regard to L-shell vacancy production and L-K electron capture for Ar targets. In addition, K-K electron capture cross sections were measured for 1.0 to 2.0 Mev 42He^_ ions on CH_4.

Typescript (photocopy). / Digitized by Kansas Correctional Industries

Typescript (photocopy). / Digitized by Kansas Correctional Industries

In attempts to explore the usefulness of the newly introduced electron capture dissociation (ECD) mass spectrometry for structural analysis of peptides/proteins, different fundamental aspects of the ECD method were investigated using a combination of controlled experiments and high-level theoretical calculations. The relative propensity for dissociation (RPD) of different amino acid residues were extracted from a series of ECD experiments using a common peptide model of RGGGXGGGR, where X was varied systematically among 20 common amino acid residues. Although polar and aromatic amino acid residues were found to behave differently, there exists a fair correlation between the experimental RPD values of aliphatic amino acid residues and the corresponding calculated hydrogen atom affinities of the nearby carbonyl groups. The existence of this correlation reinforces the importance of "hot hydrogen-atom model". From the same set of experiments, the side chain loss reactions of the reduced precursor ions and the zn+• species were extracted. To account for the observed secondary fragments, several generalized dissociation pathways were proposed. The energetics of these dissociation pathways were evaluated theoretically with truncated peptide models using ab initio and DFT calculations; and the kinetics of several competitive reactions were evaluated using Rice-Ramsberger-Kassel-Marcus (RRKM) calculations. / The effect of charge carriers on ECD of peptides/proteins was also studied. Peptides charged through protonation of different basic amino acid residues were found to give ECD spectra of different complexities. The formation of b-/y- and atypical internal fragment ions in peptides with histidines (and lysine, to a lesser extent) as proton carriers was attributed to the higher electron-proton recombination energy as revealed from the energy cycle diagram. Peptides charged through attachment of divalent metal ions were found to give very different ECD spectra. It was believed that typical c/z • fragments were formed from neutralization reactions involving electron-proton recombination; whereas a/b/y fragments were formed from reaction involving electron-metal ion recombination. The preference of recombination channels was somehow related to the electronic configurations of the divalent metal ions. / Fung Yi Man. / "July 2006." / Adviser: T. W. Chan. / Source: Dissertation Abstracts International, Volume: 68-08, Section: B, page: 5254. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (p. 180-185). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese. / School code: 1307.

Choy, Man Fai. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (leaves 120-123). / Abstracts in English and Chinese. / Title Page --- p.1 / Abstract (English) --- p.2 / Abstract (Chinese) --- p.3 / Acknowledgement --- p.4 / Declaration --- p.5 / Table of Content --- p.6 / Lists of Figures --- p.9 / Lists of Tables --- p.12 / List of Schemes --- p.13 / Chapter Chapter One --- Introduction / Historical perspective and overview of tandem mass spectrometry for structural biochemistry --- p.14 / Electrospray ionization (ESI) --- p.15 / Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) --- p.18 / Chapter 1.3.1 --- History of FTICR --- p.18 / Chapter 1.3.2 --- Theory of FTICR --- p.21 / Chapter 1.4 --- Sequencing of DNA fragments --- p.26 / Chapter 1.4.1 --- Conventional and mass spectrometric sequencing techniques --- p.26 / Chapter 1.4.2 --- Fragment-ion nomenclature --- p.27 / Chapter 1.4.3 --- Tandem mass spectrometry of oligonucleotide ions --- p.29 / Chapter 1.4.4 --- Electron capture dissociation of oligonucleotide ions --- p.31 / Chapter 1.5 --- Outline of the present work --- p.32 / Chapter Chapter Two --- Instrument and Experimental / Chapter 2.1 --- Instrumentation --- p.35 / Chapter 2.1.1 --- Fourier-transform ion cyclotron resonance mass spectrometer --- p.35 / Chapter 2.1.2 --- Vacuum system --- p.35 / Chapter 2.1.3 --- Nanospray ion source --- p.39 / Chapter 2.1.4 --- Ion Transfer system --- p.41 / Chapter 2.1.5 --- Infinity cell --- p.43 / Chapter 2.1.6 --- Electron emission source --- p.44 / Chapter 2.2 --- Experimental section --- p.47 / Chapter 2.2.1 --- Simple acquisition pulse program --- p.47 / Chapter 2.2.2 --- ECD pulse program --- p.49 / Chapter Chapter Three --- Production of Doubly-prontonated Oligonucleotide ions using Nanospray Ionization / Chapter 3.1 --- Introduction --- p.52 / Chapter 3.2 --- Experimental and instrumental section --- p.53 / Chapter 3.2.1 --- Materials --- p.53 / Chapter 3.2.2 --- Sample preparation --- p.53 / Chapter 3.2.3 --- Instrumentation --- p.54 / Chapter 3.3 --- Results and discussion --- p.54 / Chapter 3.3.1 --- Effect of the concentration of ammonium formate --- p.54 / Chapter 3.3.2 --- Effects of the anionic pair of the ammonium salts --- p.57 / Chapter 3.3.3 --- Effects of solvent composition --- p.64 / Chapter 3.3.4 --- Effects of analyte concentration --- p.66 / Chapter 3.4 --- Conclusion --- p.68 / Chapter Chapter Four --- Electron Capture Dissociation of Model Oligonucleotides / Chapter 4.1 --- Introduction --- p.69 / Chapter 4.2 --- Experimental and instrumental section --- p.70 / Chapter 4.2.1 --- Materials --- p.70 / Chapter 4.2.2 --- Sample preparation --- p.70 / Chapter 4.2.3 --- Instrumentation --- p.71 / Chapter 4.2.4 --- Method of calculations --- p.71 / Chapter 4.3 --- Results and discussion --- p.72 / Chapter 4.3.1 --- "ECD of d(CCCCC), d(CCAAC), d(CCTTC) and d(CCGGC)" --- p.72 / Chapter 4.3.1.1 --- General features --- p.72 / Chapter 4.3.1.2 --- Protonated nucleobases and nucleoside-like fragments --- p.73 / Chapter 4.3.1.3 --- Doubly-charged fragment ions --- p.79 / Chapter 4.3.2 --- Theoretical calculation of electron capture affinities of common functionalities in oligonucleotides --- p.80 / Chapter 4.3.3 --- Electron capture dissociation of C/T binary-based oligonucleotides --- p.81 / Chapter 4.3.3.1 --- "ECD of d(CTCTC), d(TCCCT) and d(CTTTC)" --- p.84 / Chapter 4.3.3.2 --- ECD of d(CCCCT) and d(TCCCC) --- p.84 / Chapter 4.3.4 --- Mechanistic implications --- p.89 / Chapter 4.4 --- Conclusion --- p.99 / Chapter Chapter Five --- Electron Capture Dissociation of a Series of G/T Binary Base of Oligonucleotides / Chapter 5.1 --- Introduction --- p.100 / Chapter 5.2 --- Experimental and instrumental section --- p.100 / Chapter 5.2.1 --- Materials --- p.100 / Chapter 5.2.2 --- Sample preparation --- p.100 / Chapter 5.2.3 --- Instrumentation --- p.101 / Chapter 5.3 --- Results and discussion --- p.101 / Chapter 5.3.1 --- Electron capture dissociation of d(GGGGG) --- p.101 / Chapter 5.3.2 --- Electron capture dissociation of G/T binary-based oligonucleotides --- p.104 / Chapter 5.3.2.1 --- "ECD of d(GTGTG), d(GTTTG) and d(TGGGT)" --- p.104 / Chapter 5.3.2.2 --- ECD of d(GGGGT) and d(TGGGG) --- p.107 / Chapter 5.3.3 --- Mechanistic implications --- p.110 / Chapter 5.4 --- Conclusion --- p.117 / Chapter Chapter Six --- Conclusion Remarks --- p.118 / References --- p.120 / Appendix A --- p.124 / Appendix B --- p.127