Note: From Genome to Proteome -- Contents -- Reviews -- Proteome Analysis: A Pathway to the Functional Analysis of Proteins -- Diagnosis of cellular states of microbial organisms using proteomics -- Candida albicans pathogenicity: A proteomic perspective -- Proteomics for genetic and physiological studies in plants -- Proteomics In human disease: Cancer, heart and Infectious diseases -- Genotypes and phenotypes -- Replication-Induced protein synthesis and Its importance to proteomics -- Advances In proteln solubillsatlon for two-dimensional electrophoresis -- Proteomics and automation -- Genomes and proteomes: Towards a multidimensional view of biology -- Sample preparation and solubilization -- The potential use of laser capture microdissection to selectively obtain distinct populations of cells for proteomic analysis - Preliminary findings -- Extractlon of Escherichia coli proteins with organic solvents prior to two-dimensional electrophoresis -- Towards the recovery of hydrophobic proteins on two-dimensional electrophoresis gels -- Developments in electrophoresis -- Recent developments In two-dimensional gel electrophoresis with immobilized pH gradients: Wide pH gradients up to pH 12, longer separation distances and simplified procedures -- Steady-state electrolysis of a solution of nonamphotheric compounds -- Modified lmmobillzed pH gradient gel strip equilibration procedure in SWISS-2DPAGE protocols -- Microchannel networks for electrophoretic separations -- Detection and quantitation -- Proteome analysis of polyacrylamide gel-separated proteins visualized by reversible negative staining using lmidazole-zinc salts -- Studies of quantitative analysis of protein expression in Saccharomyces cerevisiae -- Mass spectrometry -- High sensitivity mass spectrometric methods for obtaining intact molecular weights from gel-separated proteins. , Method for ldentlfication and quantitative analysis of protein lysine methylation using matrix-assisted laser desorption/ionization - time-of-flight mass spectrometry and amino acid analysis -- Proteome data analysis and management -- New algorithmic approaches to protein spot detection and pattern matching in two-dimensional electrophoresis gel databases -- Mining protein data from two-dimensional gels: Tools for systematic post-planned analyses -- Prokaryotes and yeast -- Effects of Interferon gamma on Chlamydia trachomatis serovar A and L2 protein expression Investigated by two-dimensional gel electrophoresis -- Induction of heat shock proteins in response to primary alcohols In Acinetobacter calcoaceticus -- Characterization of perlplasmic Escherichia coli protein expression at high cell densities -- Proteome analysis of factor for inversion stIlmulation (Fis) overproductlon In Escherichia coli -- Investigation of translation dynamics under cell-free protein blosynthesis conditions using high-resolutlon two-dimensional gel electrophoresis -- Regulation of virulence genes by environmental signals In Salmonella typhimurium -- Proteome analysis of the model microsymbiont Sinorhizoblum meliloti: Isolation and characterlsation of novel proteins -- Comparison of yeast cell protein solubilizatlon procedures for two-dimensional electrophoresis -- Biological Fluids -- A nondenaturing protein map of human plasma proteins correlated wlth a denaturing polypeptide map combining techniques of micro two-dimensional gel electrophoresis -- Proteins of rat serum: III. Gender-related differences in protein concentration under baseline conditions and upon experimental lnflammation as evaluated by two-dimensional electrophoresis -- Proteins of rat serum IV. Time-course of acutcphase protein expression and Its modulation by indomethacine. , improved two-dimensional gel electrophoresis representation of serum proteins by using ProtoClearTM -- ldentlflcation of proteins In a human pleural exudate using two-dimensional preparative liquid-phase electrophoresis and matrix-assisted laser desorption/Ionization mass spectrometry -- Two-dimensional polyacrylamide gel electrophoresis map of bovine ovarian fluid proteins -- Two-dimenslonal electrophoresis and computer imaging: Quantitatlon of human milk casein -- Analysis of tear protein patterns by a neural network as a diagnostlcal tool for the detection of dry eyes -- Demonstratlon of different forms of the anti-inflammatory proteins Iipocortin-1 and Clara cell protein-16 In human nasal and bronchoalveolar lavage fluids -- Eukaryotic cells and tissue -- A two-dimensional electrophoresls database of rat heart proteins -- Bovine dilated cardiomyopathy: Proteomic analysis of an animal model of human dilated cardiomyopathy -- Two-dimensional map of human brain proteins -- Analysis of proteins from membrane-enriched cerebellar preparations by two-dimensional gel electrophoresis and mass spectrometry -- Decreased levels of synaptosomal associated protein 25 in the brain of patients with Down Syndrome and Alzheimer's disease -- A proteome analysis of livers from obese (ob/ob) mice treated with the peroxisome prollferator WY14,643 -- Regional protein alterations in rat kidneys induced by lead exposure -- Functional proteomics of signal transduction by membrane receptors -- Modulation of signal transduction pathways and global protein composition of macrophages by ionizing radiation -- Characterisation of stem cell expression using two-dimensional electrophoresis -- The characterization of human spermatozoa membrane proteins - surface antigens and Immunological infertility. , Mapping and identification of HeLa cell proteins separated by immobilized pH-gradient two-dimensional gel electrophoresis and construction of a two-dimenslonal polyacrylamide gel electrophoresis database -- Mapping and Identification of interferon gamma-regulated HeLa cell proteins separated by immobilized pH gradient two-dimensional gel electrophoresis -- A two-dimensional protein map of Chinese hamster ovary cells -- Two-dimensional gel electrophoresis as analytical tool for identifying Candida albicans Immunogenic proteins -- Biochemical analysis of membrane proteins from an early maturatlon stage of phagosomes -- A computer-assisted two-dimensional gel electrophoresis approach for studying the variations in protein expression related to an induced functional repression of NFKB in lymphoblastold cell lines -- Technology development at the interface of proteome research and genomics: Mapping nonpolymorphic proteins on the physical map of mouse chromosomes -- Active dissociation of the fluorescent dye Hoechst 33342 from DNA in a living cell: Who could do It? -- Oncology -- Two-dlmenslonal gel analysis of protein expression In ovarian tumors shows a low degree of intratumorai heterogeneity -- The analysis of S100A9 and S100A8 expression In matched sets of rnacroscopically normal colon mucosa and colorectal carcinoma: The S100A9 and S100A8 positive cells underlie and invade tumor mass -- Characterization of colonic polyps by two-dimensional gel electrophoresis -- Protein changes associated wlth ionizing radiation-Induced apoptosis In human prostate epithelial tumor cells -- Two-dimensional electrophoresis of prostate-specific antigen in sera of men with prostate cancer or benign prostate hyperplasia -- A novel Isoform ratio switch of the polypyrimidine tract binding protein. , Glial fibrillary acidic protein and its fragments discriminate astrocytoma from oligodendroglloma -- ldentlflcatlon of HSP-60 as the specific antigen of IgM produced by BRG-lymphoma cells -- Plants -- Separation and characterization of needle and xylem maritime pine proteins -- Two-dimensional electrophoretic analysis of proteins associated with somatic embryogenesis development In Cupressus sempervirens L -- Index.

Note: Front Cover -- Gel Electrophoresis of Proteins -- Copyright Page -- Table of Contents -- Preface -- List of Contributors -- List of Abbreviations -- Chapter 1. Steady-state Gel Electrophoresis Systems -- 1.1 Introduction -- 1.2 Historical Developments -- 1.3 Fundamental Steady-state Electrophoresis Systems -- 1.4 Fundamental Properties of Steady-state Electrophoresis Systems -- 1.5 Nomenclature and Definitions -- 1.6 Conductivity -- 1.7 Equations for Calculation of System Composition -- 1.8 Isotachophoresis -- 1.9 Moving Boundary Electrophoresis -- 1.10 Isoelectric Focusing Systems -- Acknowledgements -- References -- Chapter 2. One-dimensional PAA-gel Electrophoretic Techniques to Separate Functional and Denatured Proteins -- 2.1 Introduction -- 2.2 Structure and Physico-chemical Properties of Polyacrylamide Gels -- 2.3 Analytical Polyacrylamide Gel Electrophoresis -- 2.4 Affinity Electrophoresis -- Acknowledgments -- References -- Chapter 3. Conventional Isoelectric Focusing and Immobilised pH Gradients -- 3.1 Introduction -- 3.2 The Principles of IEF -- 3.3 IEF in Agarose Matrices -- 3.4 IEF in Polyacrylamide Matrices -- 3.5 Titration Curves -- 3.6 Production of Narrow pH Gradients -- 3.7 Measurements of pH Gradients -- 3.8 Trouble Shooting -- 3.9 Artefacts: a Unified View -- 3.10 The Chemicals -- the Immobiline Matrix -- 3.11 Narrow and Ultra-narrow pH Gradients -- 3.12 Extended pH Gradients -- 3.13 On Buffering Capacity and Ionic Strength -- 3.14 On Electro-endosmosis -- 3.15 Polymerisation Kinetics -- 3.16 Methodology: Casting an Immobiline Gel -- 3.17 Artefacts -- 3.18 Conclusions -- Acknowledgments -- References -- Chapter 4. High Resolution Two-dimensional Polyacrylamide-gel Electrophoresis -- 4.1 Introduction -- 4.2 Two-dimensional Electrophoresis under Non-denaturing Conditions. , 4.3 Denaturing 2D Systems using Electrophoresis in both Dimensions -- 4.4 The O'Farrell System -- 4.5 Sample Preparation and Solubilisation -- 4.6 IEF Dimension -- 4.7 New Alternatives for the First Dimension of 2D PAGE -- 4.8 Equilibration -- 4.9 SDS Dimension -- 4.10 Visualisation, Detection and Analysis -- 4.11 Heterogeneity and Artefacts -- 4.12 Estimates of Resolution -- 4.13 Applications -- 4.14 2D-PAGE and the Study of Human Genetic Disorders -- Acknowledgments -- References -- Chapter 5. Immunoelectrophoretic Methods -- 5.1 Introduction -- 5.2 Historical Background -- 5.3 Theory -- 5.4 General Conditions and Guidelines -- 5.5 Contemporary Methods -- 5.6 Applicability of Immunoelectrophoretic Methods -- 5.7 Advantages and Drawbacks -- References -- Chapter 6. In situ Peptide Mapping of Proteins and Polypeptides Separated by Polyacrylamide Gel Electrophoresis -- 6.1 Introduction -- 6.2 Primary Gel Systems -- 6.3 Storage, Rehydration and Equilibration -- 6.4 Protein Cleavage -- 6.5 Secondary Gel Systems -- 6.6 Detection -- 6.7 Evaluation -- References -- Chapter 7. Protein Staining and Detection Methods -- 7.1 Historical Introduction -- 7.2 Post-Electrophoretic Organic Protein Stains -- 7.3 Pre-electrophoretic Organic Stains -- 7.4 Silver Stains -- 7.5 Enzyme Stains -- 7.6 Detection of Radioactive Proteins -- 7.7 Detection of Protein-bound Trace Elements -- 7.8 Detection of Proteins on a Support Matrix after Electroblotting -- 7.9 Conclusion -- Acknowledgments -- References -- Chapter 8. Quantifying Patterns from Two-dimensional PAGE -- 8.1 Introduction -- 8.2 Basic Outlines -- 8.3 Detectors -- 8.4 Scanning Method and Speeds of Collection -- 8.5 Collecting Data -- 8.6 Programming Languages -- 8.7 Numerical Analyses -- 8.8 Reducing Data to Models -- 8.9 Presentation of Data -- Appendices -- References -- Index.

Note: Intro -- Clinical Proteomics -- Contents -- Editor's Overview -- Acknowledgements -- List of Contributors -- I Technologies -- 1 Preanalytical Issues in Clinical Proteomic Studies -- 1.1 Introduction -- 1.2 Preanalytical Factors -- 1.2.1 Biological Variation -- 1.2.1.1 Intrinic Influences/Factors -- 1.2.1.2 Extrinsic Influences/Factors -- 1.2.2 Technical Variables -- 1.2.2.1 Specimen/Sample Collection Mode -- 1.2.2.2 Type of Sample Container -- 1.2.2.3 Sample Processing and Handling Conditions -- 1.2.2.4 Sample Storage -- 1.3 Summary and Concluding Remarks -- 2 Protein Separation by Two-Dimensional Electrophoresis -- 2.1 Introduction -- 2.2 2DE: Protein Solubilization and Sample Preparation -- 2.3 2DE: Protein Separation -- 2.3.1 Focusing in the First Dimension -- 2.3.2 Advances in IEF -- 2.4 Improving Proteomic Coverage by Subcellular Fractionation -- 2.5 Protein Detection and Image Analysis -- 2.6 The Future of 2DE -- 3 Protein Separation: Liquid Chromatography -- 3.1 Introduction -- 3.2 Liquid Chromatography -- 3.2.1 HPLC Separation Principles -- 3.2.2 Reversed-Phase LC (RPLC, 1DLC) -- 3.2.3 Affinity Chromatography -- 3.2.4 Size-Exclusion Chromatography -- 3.2.5 Ion-Exchange Chromatography -- 3.2.6 Two-Dimensional LC -- 3.2.6.1 Chromatofocusing to Reversed Phase -- 3.2.6.2 Ion-Exchange-Reversed-Phase Liquid Chromatography -- 3.2.7 Three-Dimensional Liquid Chromatography -- 3.2.8 LC Image Analysis Requirement -- 3.2.9 Mass Spectrometry for LC -- 3.2.9.1 MALDI-TOF MS -- 3.2.9.2 ESI-MS/MS -- 3.3 Conclusions -- 4 HPLC in Protein Discovery -- 4.1 Introduction -- 4.2 LC-Based Approaches in Peptide Mass Mapping -- 4.3 LC-Based Approaches in Protein Mapping -- 4.4 Orthogonal 2D HPLC Separations -- 4.5 Conclusion -- 5 IEF Analysis of Peptides for Biomarkers Discovery -- 5.1 Introduction -- 5.2 Background -- 5.2.1 Isoelectric Focusing. , 5.2.2 Shotgun Proteomics -- 5.2.3 Shotgun IEF -- 5.3 Shotgun IEF Workflow -- 5.4 Applications -- 5.5 Discussion and Outlook -- 6 Capillary Electrophoretic Separations for Clinical Proteomics -- 6.1 Introduction -- 6.2 (Single-Dimension) Capillary Electophoretic Separation -- 6.3 Capillary Electrophoresis-Based Multidimensional Separations -- 6.3.1 Capillary Liquid Chromatography-Capillary Electrophoresis -- 6.3.2 Capillary Electrophoresis-Capillary Electrophoresis -- 6.3.3 Capillary Electrophoresis-Liquid Chromatography -- 6.3.3.1 Characterization of Human Saliva Proteome -- 6.3.3.2 Targeted Tissue Proteomics -- 6.4 Conclusions -- 7 Quantitative Proteomics Using Nano-LC with High Accuracy Mass Spectrometry -- 7.1 Introduction -- 7.2 Fundamentals of a High Mass Accuracy-Based LC-MS Approach -- 7.3 Nano-LC-MS for Enhanced Sensitivity and Dynamic Range Coverage -- 7.4 Further Developments for Increasing Proteomic Throughput -- 7.5 Obtaining More Robust Quantitative Proteomic Measurements -- 7.6 Summary and Perspective -- 8 Antibody Microarrays for Protein and Glycan Detection -- 8.1 Introduction -- 8.2 Antibody Preparation and Microarray Production -- 8.3 Sandwich Assays with Fluorescence Detection -- 8.4 Antibody Microarrays with Lectin Detection -- 8.5 Conclusion -- 8.6 Detailed Protocols -- 9 Biomarker Identification: The Role of Experimental Design, Statistics, and Data Sharing -- 9.1 Introduction -- 9.2 Experimental Designs for Biomarker Discovery -- 9.3 Identification of Biomarker Proteins -- 9.4 Biomarker Validation and the Issue of Data Sharing -- 9.5 Conclusions -- II Cancer -- 10 Applications of Stable Isotope Tagging Based Quantitative Proteomics in Cancer Research -- 10.1 Introduction -- 10.2 Stable Isotope Tagging Methods -- 10.2.1 Chemical Labeling of Stable Isotope Tags -- 10.2.2 Biological Incorporation of Stable Isotope Tags. , 10.3 Applications in Studies of Tissue Samples -- 10.3.1 Whole Tumor Tissue Labeled with ICAT -- 10.3.2 Whole Tumor Tissue Labeled with ICAT and iTRAQ -- 10.3.3 Isolated Tumor Cells Labeled with ICAT -- 10.3.4 Isolated Tumor Cells Labeled with (16)O/(18)O -- 10.4 Applications in Studies of Bodily Fluids -- 10.4.1 Pancreatic Juice Labeled with ICAT -- 10.4.2 Nipple Aspirate Fluid Labeled with ICAT -- 10.4.3 CSF -- 10.5 Applications in Studies of Cell Lines -- 10.5.1 Ovarian Cancer Cell Lines Labeled with ICAT -- 10.5.2 Breast Cancer Cell Lines Labeled with (18)O Labeling -- 10.5.3 Prostate Cancer Cell Lines Labeled with SILAC -- 10.5.4 Secretome by Pancreatic Cancer Cell Line Labeled with SILAC -- 10.6 Applications in Studies of Protein Interaction -- 10.7 Applications in Studies of Posttranslational Modifications (PTM) -- 10.8 Summary -- 11 Two-Dimensional Liquid Separations, Protein Microarrays, and Mass Spectrometry in Comprehensive Analysis of Posttranslational Modifications and Biomarker Discovery in Cancers -- 11.1 Challenges in Biomarker Discovery: The Emerging Role of Posttranslational Modifications -- 11.2 Proteomics in Disease Research -- 11.3 The Problem of Identifying and Characterizing Posttranslational Modifications: Current Efforts -- 11.4 Microarrays in Proteomic Investigations -- 11.5 A Comprehensive Method Combining Liquid Separations, Microarrays, and Mass Spectrometry -- 11.6 2D Liquid-Based Separations and Mass Mapping -- 11.7 Posttranslational Modification (PTM) Analysis -- 11.8 Phosphorylation -- 11.9 Glycosylation -- 11.10 Autoimmune (Humoral) Response Studies -- 11.11 Future of a 2DLC, Microarray Methodologies in Discovery and Diagnostics -- 12 Development and Use of Reversed-Phase Protein Microarrays for Clinical Applications -- 12.1 Introduction -- 12.2 The Growing Role of Protein Arrays in Molecular Diagnostics. , 12.3 Reversed-Phase Arrays: Enabling Technology for Patient-Tailored Therapeutics -- 12.4 Use of Reversed-Phase Arrays for Signal Pathway Profiling of Human Cancer -- 12.5 Use of Reversed-Phase Arrays: A View to the Future -- 13 Cyclin-Dependent Kinase Inhibitors and Cancer: Usefulness of Proteomic Approaches in Assessment of the Molecular Mechanisms and Efficacy of Novel Therapeutics -- 13.1 Introduction -- 13.2 Proteomic Analysis of Cancer Cells Responding to the Synthetic CDKI -- 13.3 Two-Dimensional Protein Maps of Cancer Cells Treated by CDKI -- 13.3.1 Model of Hematological Malignancy: CEM T-Lymphoblastic Leukemia -- 13.3.2 Solid Tumor Model: A549 Lung Adenocarcinoma Cells -- 13.4 Evaluation of the Protein Maps: Possible Pathways Relevant to Anticancer Effects of CDK Inhibition -- 13.4.1 Candidate Biomarkers Identified Using the Hematological Malignancy Model -- 13.4.2 Candidate Biomarkers Identified Using the Solid Tumor Model -- 13.5 Biomarker Validation Studies Focused on the crkl Protein -- 13.6 Conclusions -- III Cardiac Disease -- 14 Diagnostic Markers for Monitoring Heart Transplant Rejection -- 14.1 Introduction -- 14.2 Acute Rejection -- 14.3 Chronic Rejection -- 14.4 Cardiopulmonary Bypass -- 14.5 Conclusions -- 15 The Study of Microheterogeneity in Human Plasma Proteins: Application to Acute Myocardial Infarction -- 15.1 Background -- 15.2 Technical Approach -- 15.3 Programmatic Study of Disease: Population Proteomics Versus Myocardial Infarction -- 15.3.1 Preliminary Screening, (Putative) Biomarker Discovery and Identification -- 15.3.2 Verification -- 15.3.3 Knowledge Assembly and Next-Generation Assay Design -- 15.3.4 Data Generation -- 15.3.5 Data Analysis -- 15.3.6 Blind and Randomized Challenge of Final Assay -- 15.4 Summary -- 16 Discovery of Biomarkers for Cardiovascular Diseases. , 16.1 Current Proteomic Technologies Available for CVD Biomarker Searches -- 16.2 Challenging Issues for Proteomic Profiling -- 16.3 Screening Blood for Biomarkers -- 16.4 Tissue Surveys -- 16.5 The Value of Animal Models -- 16.6 After Technology Platform and Sample Selection: What Makes a Good Biomarker? -- 16.7 Ongoing Considerations -- 16.8 Outlook -- 17 Development of Biomarker Development Pipeline: Search for Myocardial Ischemia Biomarkers -- 17.1 Introduction -- 17.2 Myocardial Ischemia and Infarction -- 17.3 Lessons Learned from Cardiac Troponin -- 17.4 Building a Biomarker Development Platform I-Discovery -- 17.4.1 High-Abundant Protein Partitioning -- 17.4.2 Utilizing Multiple Protein Separation Methods to Maximize Proteome Coverage: A Synergistic Approach -- 17.5 Validation -- 17.5.1 Technologies in Validation -- 17.5.2 Cohorts for the Validation -- 17.6 Summary -- 18 The Albuminome as a Tool for Biomarker Discovery -- 18.1 Protein-Protein Interactions and Protein-Centric Approaches in Proteomics -- 18.2 Defining the Albuminome -- 18.3 The Albuminome as a Tool in Biomarker Discovery -- 18.4 Role of the Albuminome in Cardiovascular Proteomics -- 18.5 Other Plasma Subproteomes -- 18.6 Conclusion -- 19 Application of Metabolomics to Cardiovascular Biomarker and Pathway Discovery -- 19.1 Introduction -- 19.2 The Birth of Metabolomics -- 19.3 Technologies to Define the Human Metabolome -- 19.4 The Diagnostic Utility of Metabolic Peak Patterns: A Call for Unambiguous Identification -- 19.5 Pathway Analysis of Metabolomic Data -- 19.6 Rationale for Metabolomic Approaches to Study Atherosclerosis and its Complications: The Role of Proinflammatory Lipid Metabolites -- 19.7 Unanticipated Roles of "Intracellular" Metabolites -- 19.8 Clinical Rationale for Applying Metabolomics to Coronary Heart Disease -- 19.9 Impediments to Human Applications. , 19.10 Application of Metabolomics to Unique Human Cardiovascular Disease Models.