Keywords:
Proteomics.
;
Electronic books.
Type of Medium:
Online Resource
Pages:
1 online resource (695 pages)
Edition:
1st ed.
ISBN:
9783527622160
URL:
https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=481597
DDC:
572.6
Language:
English
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.
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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.
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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.
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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.
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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.
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19.10 Application of Metabolomics to Unique Human Cardiovascular Disease Models.
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