Kong Kam-chuen, Ebenezer. / Thesis submitted in: July 2003. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references (leaves 131-149). / Abstracts in English and Chinese. / Abstract in English --- p.i / Abstract in Chinese --- p.ii / Table of Content --- p.iii -vii / Acknowledgement --- p.viii / List of Abbreviations --- p.ix -x / List of Tables --- p.xi / List of Figures --- p.xii -xiii / List of Appendices --- p.xiv -xv / Chapter CHAPTER 1 --- Review of Literature / Chapter 1.1 --- Peptidomic Research / Chapter 1.1.1 --- Proteomics and Genomics --- p.1-2 / Chapter 1.1.2 --- Peptidomics and Quantitative Profiling --- p.2-5 / Chapter 1.1.3 --- Proteomics and Peptidomics in Medical Research --- p.5-6 / Chapter 1.1.4 --- Application of Quantitative Peptidomic Profiling in Cancer Research --- p.6-8 / Chapter 1.2 --- Technologies for Peptidomic Studies and Limitations --- p.9-11 / Chapter 1.2.1 --- High Performance Liquid Chromatograph (HPLC) --- p.12 / Chapter 1.2.1.1 --- Basic Principle --- p.13-15 / Chapter 1.2.1.2 --- Application in Peptidomic / Proteomic Research --- p.16-17 / Chapter 1.2.2 --- Peptide Gel Electrophoresis --- p.18 -19 / Chapter 1.2.2.1 --- Basic Principle --- p.19-21 / Chapter 1.2.2.2 --- Application in Peptidomic / Proteomic Research --- p.21 -22 / Chapter 1.2.3 --- Capillary Electrophoresis (CE) --- p.23 -24 / Chapter 1.2.3.1 --- Basic Principle --- p.24-29 / Chapter 1.2.4 --- Mass Spectrometry --- p.30 / Chapter 1.2.4.1 --- Electro spray Ionization (ESI) Mass Spectrometry --- p.31 / Chapter 1.2.4.1.1 --- Basic Principle --- p.31-34 / Chapter 1.2.4.2 --- Matrix-assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry --- p.35 / Chapter 1.2.4.2.1 --- Ionization of Sample --- p.35 -38 / Chapter 1.2.4.2.2 --- Time-of-Flight (TOF) Analyzer --- p.39-40 / Chapter 1.2.4.2.3 --- Application in Peptidomic / Proteomic Research --- p.40-42 / Chapter 1.2.4.2.4 --- Isotope-Coded Affinity Tags (ICAT®) --- p.42 -46 / Chapter 1.2.4.2.5 --- Limitations --- p.46 -48 / Chapter 1.2.4.3 --- Surface Enhanced Laser Desorption/Ionization (SELDI) Mass Spectrometry --- p.49 / Chapter 1.2.4.3.1 --- Basic Principle --- p.49 -51 / Chapter 1.2.4.3.2 --- Application in Peptidomic / Proteomic Research --- p.51-52 / Chapter 1.2.4.3.3 --- Retentate Chromatography (RC) --- p.53-54 / Chapter 1.2.4.4. --- Recent Advances in Application of MALDI Technologies --- p.55 -57 / Chapter CHAPTER 2 --- Objectives --- p.58 -59 / Chapter CHAPTER 3 --- Methodologies / Chapter 3.1 --- Method Development / Chapter 3.1.1 --- Nitrocellulose (NC) Preparation --- p.60 / Chapter 3.1.2 --- Matrix Chemicals Preparation --- p.60 / Chapter 3.1.3 --- Spotting Methods --- p.61 / Chapter 3.1.4 --- Standard Preparation --- p.61 -63 / Chapter 3.1.5 --- Data Collection and Analysis --- p.64 / Chapter 3.2 --- Identification of Distinguishing Features for HCC --- p.65 / Chapter 3.2.1 --- Classification Trees --- p.65 -66 / Chapter 3.2.2 --- Statistical Analysis --- p.66 / Chapter CHAPTER 4 --- Results / Chapter 4.1 --- Optimization of Spotting Methods in Protein Quantification --- p.67 -68 / Chapter 4.1.1 --- Detection of Low-Molecular Weight Proteins / Peptides --- p.68 -71 / Chapter 4.1.2 --- Detection of High-Molecular Weight Proteins --- p.71 -74 / Chapter 4.2 --- Assay Linearity of the Nitrocellulose-MALDI-TOF MS for Peptides with Different Masses --- p.75 -84 / Chapter 4.3 --- Accuracy of Mass Measurement --- p.84 -85 / Chapter 4.4 --- Applications in Quantitative Peptidomic Profiling of Serum --- p.86 -88 / Chapter 4.5 --- Application in Tumor Marker Discovery / Chapter 4.5.1 --- Identification of Peptidomic Features For Classification Between the HCC and CLD Patients by Classification Tree Analysis --- p.89 - 92 / Chapter 4.5.2 --- Serum Levels of the Diagnostic Peptides in the HCC and CLD Patient Groups --- p.93 / Chapter 4.5.3 --- Spearman's Rank Correlation Analysis of the Diagnostic Peptides and AFP --- p.93-101 / Chapter 4.5.4 --- Combined Use of the Diagnostic Peptides and AFP in the Diagnosis of HCC --- p.102-105 / Chapter CHAPTER 5 --- Discussion --- p.106-108 / Chapter 5.1 --- Evaluation of Different Matrix Chemical and Sample Spotting Techniques / Chapter 5.1.1 --- Effect of CHCA and SA --- p.109 / Chapter 5.1.2 --- Effect of Nitrocellulose in Peptide Ions Formation --- p.110-112 / Chapter 5.2 --- MS Automation and High-Throughput Sampling --- p.113 / Chapter 5.3 --- Reproducibility and Signal Quantitations --- p.114-115 / Chapter 5.4 --- Peptidomics: The Study of Entire Peptidome --- p.116 / Chapter 5.5 --- Serum Peptides --- p.117-118 / Chapter 5.6 --- Application of Peptidomics to Discover Markers for HCC / Chapter 5.6.1 --- Hepatocellular Carcinoma --- p.119 / Chapter 5.6.2 --- Causes of HCC --- p.119-120 / Chapter 5.6.3 --- HCC Tumor Markers --- p.120-122 / Chapter 5.6.4 --- HCC Tumor Markers Identified in the Current Studies --- p.122-124 / Chapter 5.7 --- "Role of MALDI-TOF MS, SELDI-TOF MS and 2-DE in Peptidomics" --- p.125-128 / Chapter CHAPTER 6 --- Conclusion --- p.129-130 / Chapter CHAPTER 7 --- References --- p.131-140 / Chapter CHAPTER 8 --- Original Data --- p.150 / Chapter CHAPTER 9 --- Appendices --- p.151-167