Suppression of peptide ions dissociation under electron capture condition.

Wong, Pui Shuen.Thesis (M.Phil.)--Chinese University of Hong Kong, 2011.Includes bibliographical references (leaves 92-96).Abstracts in English and Chinese.Title Page --- p.iAbstract (English) --- p.iiAbstract (Chinese) --- p.iiiAcknowledgements --- p.ivTable of Contents --- p.VList of Tables --- p.viiiList of Figures --- p.ixList of Schemes --- p.xiSymbols and Abbreviations --- p.xiiDedication --- p.xivChapter Chapter 1 --- IntroductionChapter 1.1 --- Mass Spectrometry of peptides/ proteins --- p.1Chapter 1.1.1 --- Electrospray ionization of peptides/ proteins --- p.3Chapter 1.2 --- Tandem mass spectrometry of peptides/ proteins --- p.4Chapter 1.2.1 --- Nomenclature of peptide fragment ions --- p.5Chapter 1.2.2 --- Slow heating methods for MSn --- p.6Chapter 1.2.2.1 --- Collision induced dissociation --- p.7Chapter 1.2.3 --- "Electron based ion activation for MS""" --- p.8Chapter 1.3 --- Electron Capture Dissociation --- p.9Chapter 1.3.1 --- ECD mechanism for protonated peptide ions --- p.10Chapter 1.3.2 --- ECD efficiency --- p.12Chapter 1.3.3 --- ECD of metal ions-adducted peptide --- p.13Chapter 1.4 --- Overview of present work --- p.14Chapter Chapter 2 --- "Instrumentation, Experimental and Calculations"Chapter 2.1 --- Fourier-transform Ion Cyclotron Resonance Mass Spectrometer --- p.15Chapter 2.1.1 --- Basic principle of FTICR-MS --- p.15Chapter 2.1.2 --- The instrument --- p.19Chapter 2.1.2.1 --- Vacuum system --- p.19Chapter 2.1.2.2 --- Nanospray source --- p.24Chapter 2.1.2.3 --- Electrostatic ion focusing system --- p.26Chapter 2.1.2.4 --- Infinity´ёØ Cell --- p.28Chapter 2.1.2.5 --- Electron emission source --- p.29Chapter 2.1.2.6 --- Data acquisition system --- p.31Chapter 2.2 --- Experimental --- p.31Chapter 2.2.1 --- Acquisition pulse program --- p.31Chapter 2.2.1.1 --- Simple ESI acquisition pulse program (MS experiment) --- p.31Chapter 2.2.1.2 --- ESI-ECD acquisition pulse program (MS experiment) --- p.34Chapter 2.2.2 --- Molecular mechanics calculation --- p.36Chapter Chapter 3 --- Structural Parameters Affecting Suppression of N-Ca Cleavages of Peptides Ions after Electron CaptureChapter 3.1 --- Introduction --- p.37Chapter 3.2 --- Experimental section --- p.39Chapter 3.3 --- Results and Discussion --- p.40Chapter 3.3.1 --- Peptides with three arginine residues --- p.40Chapter 3.3.1.1 --- General ECD mass spectra features --- p.40Chapter 3.3.1.2 --- Comparison of the extent of suppression of triariginated and diarginated model peptides ions --- p.46Chapter 3.3.2 --- Peptides with histidine and lysine as proton carriers --- p.47Chapter 3.3.2.1 --- General features of ECD mass spectra --- p.47Chapter 3.3.2.2 --- Comparison of ECD behavior of peptide ions with different proton carrier --- p.50Chapter 3.3.3 --- Peptides with various chain length --- p.53Chapter 3.3.3.1 --- General ECD mass spectra features --- p.53Chapter 3.3.3.2 --- Reactivation of [M+2H]+* by collision activation --- p.57Chapter 3.3.3.3 --- Significance of glutamic acid residues --- p.57Chapter 3.3.3.4 --- Results of conformational searches --- p.60Chapter 3.4 --- Conclusions --- p.64Chapter Chapter 4 --- Investigation of the Role of Conformation of Peptide Ions in Suppression of Backbone fragmentationChapter 4.1 --- Introduction --- p.67Chapter 4.2 --- Experimental section --- p.69Chapter 4.3 --- Results and Discussion --- p.70Chapter 4.3.1 --- Peptide with N-methylated amino acid residues --- p.70Chapter 4.3.1.1 --- General features of ECD mass spectra --- p.70Chapter 4.3.1.2 --- Comparison between normal and N-methylated peptide ions under ECD --- p.72Chapter 4.3.2 --- Peptides with proline residues vi --- p.73Chapter 4.3.2.1 --- General ECD mass spectra features --- p.73Chapter 4.3.2.2 --- Comparison of ECD of peptide ions with and without proline residues --- p.76Chapter 4.3.3 --- Transition metal ions as charge carriers --- p.80Chapter 4.3.3.1 --- General ECD mass spectra features --- p.80Chapter 4.3.3.2 --- Comparison of ECD behavior using proton and metal ions as charge carrier --- p.85Chapter 4.4 --- Conclusions --- p.87Chapter Chapter 5 --- Conclusions --- p.90References --- p.92Chapter Appendix I --- Twenty common amino acids --- p.97Chapter Appendix II --- Pulse programs for MS and MSn experiments --- p.9