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