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Proteomic and Metabolomic Approaches to Biomarker Discovery
- 1st Edition - May 20, 2013
- Editor: Haleem J. Issaq
- Language: English
- Hardback ISBN:9 7 8 - 0 - 1 2 - 3 9 4 4 4 6 - 7
- eBook ISBN:9 7 8 - 0 - 1 2 - 3 9 4 7 9 5 - 6
Proteomic and Metabolomic Approaches to Biomarker Discovery demonstrates how to leverage biomarkers to improve accuracy and reduce errors in research. Disease biomarker discovery… Read more
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Request a sales quoteProteomic and Metabolomic Approaches to Biomarker Discovery demonstrates how to leverage biomarkers to improve accuracy and reduce errors in research. Disease biomarker discovery is one of the most vibrant and important areas of research today, as the identification of reliable biomarkers has an enormous impact on disease diagnosis, selection of treatment regimens, and therapeutic monitoring. Various techniques are used in the biomarker discovery process, including techniques used in proteomics, the study of the proteins that make up an organism, and metabolomics, the study of chemical fingerprints created from cellular processes.
Proteomic and Metabolomic Approaches to Biomarker Discovery is the only publication that covers techniques from both proteomics and metabolomics and includes all steps involved in biomarker discovery, from study design to study execution. The book describes methods, and presents a standard operating procedure for sample selection, preparation, and storage, as well as data analysis and modeling. This new standard effectively eliminates the differing methodologies used in studies and creates a unified approach. Readers will learn the advantages and disadvantages of the various techniques discussed, as well as potential difficulties inherent to all steps in the biomarker discovery process.
A vital resource for biochemists, biologists, analytical chemists, bioanalytical chemists, clinical and medical technicians, researchers in pharmaceuticals, and graduate students, Proteomic and Metabolomic Approaches to Biomarker Discovery provides the information needed to reduce clinical error in the execution of research.
- Describes the use of biomarkers to reduce clinical errors in research
- Includes techniques from a range of biomarker discoveries
- Covers all steps involved in biomarker discovery, from study design to study execution
Biochemists, analytical chemists, bioanalytical chemists, biologists, medical technicians, clinical technicians, researchers in pharmaceuticals, graduate students and all interested in the field of biomarkers research.
Preface
List of Contributors
Chapter 1. Biomarker Discovery: Study Design and Execution
Abbreviations
Introduction
Definitions
The Current State of Biomarker Discovery
Study Design and Execution
Errors in Study Design
Errors in Study Execution
Specificity of Proteins as Biomarkers
Statistical Data Analysis
Recommendations
Concluding Remarks and Recommendations
References
Chapter 2. Proteomic and Mass Spectrometry Technologies for Biomarker Discovery
Nonstandard Abbreviations
Introduction
Protein Biomarker Discovery and Development Pipeline
Proteomic Samples
Protein Identification by Mass Spectrometry
Post-Translational Modifications as Disease Biomarkers
Protein Quantification by Mass Spectrometry
Biomarker Verification
Biomarker Validation
Limitations of Mass Spectrometry for Protein Biomarker Discovery
Conclusions and Future Outlook: Integrated Biomarker Discovery Platform
References
Chapter 3. Tissue Sample Preparation for Proteomic Analysis
Introduction
Types of Tissues Available for MS-Based Proteomics
Tissue Disruption/Homogenization
Extraction/Solubilization Buffers
Concluding Remarks
References
Chapter 4. Sample Preparation in Global Metabolomics of Biological Fluids and Tissues
Abbreviations
Introduction
An Ideal Sample Preparation Method for Global Metabolomics?
Sample Preparation Methods for Biofluids
Tissue Metabolomics
New Trends in Sample Preparation for Global Metabolomics
Conclusions and Future Perspective
References
Chapter 5. Serum and Plasma Collection: Preanalytical Variables and Standard Operating Procedures in Biomarker Research
Introduction
Importance of Preanalytical Variables
Standard Operating Procedures (SOPS)
Sample Selection Considerations
Human Blood and Its Components
Other Biosamples
Blood-Borne Pathogens, Universal Precautions, and Safety
Human Subject Research Protections
Conclusions
References
Chapter 6. Current NMR Strategies for Biomarker Discovery
Introduction: Why NMR?
NMR Hardware Advancement
Sample Preparation for NMR Analysis
One-Dimensional NMR Methods: 1H, 13C, 31P
2D Methods
Targeted Metabolic Profiling
High-Resolution Magic Angle Spinning (HR-MAS) NMR Spectroscopy
Magnetic Resonance Spectroscopy (MRS)
NMR Data Processing and Preparation for Statistical Analysis
NMR Metabolite Identification
Future Directions and Conclusion
References
Chapter 7. Using Data-Independent Mass Spectrometry to Extend Detectable Dynamic Range without Prior Fractionation
Introduction
PAcIFIC and Quantification
Proteome Profiling with PAcIFIC
Perspectives
References
Chapter 8. Gas Chromatography/Mass Spectrometry-Based Metabonomics
Introduction
GC/MS in Metabonomics
Strategies to Address Large-Scale Metabonomic Investigations
Conclusion and Future Outlook
References
Chapter 9. Liquid Chromatographic Methods Combined with Mass Spectrometry in Metabolomics
Introduction
Chromatographic Methods for Metabolite Profiling
Detection
Quality Control, Data Analysis, and Biomarker Detection
Metabolite Identification and Biomarker Validation
Conclusions
References
Chapter 10. Capillary Electrophoresis–Mass Spectrometry for Proteomic and Metabolic Analysis
Analysis of Metabolite Profiles Using Capillary Electrophoresis–Mass Spectrometry
Analysis of Protein Expression Levels Using Capillary Electrophoresis–Mass Spectrometry
Conclusion
References
Chapter 11. Current Gel Electrophoresis Approaches to Low-Abundance Protein Marker Discovery
Introduction
The Evolution of 2-DE Toward Proteomics Applications
Low-Abundance Proteins Are Not Resolved by 2-DE Alone
Enhancing Low-Abundance Proteins
The Discovery of Protein Markers with 2-DE and Its Association with Low-Abundance Protein Enrichment
Conclusions
Dedication
References
Chapter 12. Two-Dimensional Difference in Gel Electrophoresis for Biomarker Discovery
Introduction
Gel Electrophoresis: Historical Perspective
Two-Dimensional Differential In-Gel Electrophoresis
Strengths and Weaknesses of 2D-PAGE and 2D-DIGE
Application of 2D-DIGE to Biomarker Discovery
Conclusions
References
Chapter 13. Affinity Targeting Schemes for Biomarker Research
Introduction
Affinity Targeting Methods
Single Gene Expression Product Selection
Post-Translational Modifications
Abundant Protein Removal
Conclusions
References
Chapter 14. Asp-Selective Microwave-Supported Acid Proteolysis
Introduction
Aspartate-Selective Acid Proteolysis
Microwave-Supported Asp-Selective Acid Proteolysis
Methods Development with Microwave-Supported Acid Hydrolysis
Applications of Microwave-Supported Acid Hydrolysis
Advantages and Disadvantages of Microwave-Supported Asp-Selective Acid Proteolysis
References
Chapter 15. Sample Depletion, Fractionation, and Enrichment for Biomarker Discovery
Introduction
Depletion
Fractionation Procedures for Proteins and Metabolites
Affinity Chromatography
Isoelectric Focusing
Size Exclusion Chromatography
Conclusions
References
Chapter 16. Protein and Metabolite Identification
Protein Identification
Metabolite Identification in Global Metabolomics
References
Chapter 17. Quantitative Proteomics in Development of Disease Protein Biomarkers
Introduction
Quantitative Proteomic Profiling for Protein Biomarker Discovery
Targeted Proteomic Validation of Biomarker Candidates
Analyte Multiplexing and Sample Throughput
Conclusion
References
Chapter 18. Mass Spectrometry and NMR Spectroscopy–Based Quantitative Metabolomics
Metabolomics
Comparative Chemometric Analysis versus Quantitative Metabolomics
Mass Spectrometry
NMR Spectroscopy
Conclusions
References
Chapter 19. Multivariate Analysis for Metabolomics and Proteomics Data
Study 1: Cancer Detection by Proteomics
Study 2: Detection of Heart Disease by Metabolomics
Conclusions
References
Chapter 20. Top-Down Mass Spectrometry for Protein Molecular Diagnostics and Biomarker Discovery
Introduction
Mass Spectrometry Hardware for Top-Down
Sample Preparation and Separations
Informatics
Current Status
Conclusion
References
Chapter 21. A Role for Protein–Protein Interaction Networks in the Identification and Characterization of Potential Biomarkers
Introduction
Network Analysis Using Protein–Protein Interaction
Protein–Protein Interaction Databases
Common Experimental Methodologies to Interrogate Protein–Protein Interactions
Addressing the Background Problem
Conclusion
References
Chapter 22. Reverse Phase Protein Microarray Technology: Advances into the Clinical Research Arena
Introduction
Origin of RPMA Technology
RPMA in the Molecular Oncology Clinic
Validation of Mass Spectrometry–Discovered Candidate Biomarkers by RPMA
Conclusions and Vision for the Future
References
Chapter 23. Autoantibodies and Biomarker Discovery
Introduction
Proteomics Methods for the Detection of Autoantibodies
Association of Autoantibodies with Disease States
Challenges and Future Development
References
Chapter 24. MicroRNAs and Biomarker Discovery
Abbreviations
Introduction
Basics of miRNA Biology, Function, and Detection
Examples for MIRNA Biomarker Discovery Studies
Conflict of Interest
References
Chapter 25. Imaging Mass Spectrometry of Intact Biomolecules in Tissue Sections
Introduction
Matrix Application
Protein Analysis
Peptides and Protein Digests
Lipid Analysis
Drug Analysis
3D Imaging
High-Speed Imaging
Conclusions and Perspectives
References
Chapter 26. Mass Spectrometry–Based Approach for Protein Biomarker Verification
Abbreviations
Introduction
MRM-MS Assay Generation for Protein Quantitation
MRM-MS Assay Performance Characteristics for Biomarker Verification
Sample Enrichment Strategies for Improving Biomarker Verification
Mass Spectrometry–Based Strategies to Improve Biomarker Verification
Stable Isotope-Labeled Internal Standards Used
Bioinformatics Software for MRM-MS Assays and Biomarker Verification
Selected Biomarker Verification Applications Based on MRM-MS
Conclusions and Perspectives
References
Chapter 27. Mass Spectrometry Metabolomic Data Handling for Biomarker Discovery
Metabolomics for Biomarker Discovery
Mass Spectrometry-Based Metabolomics
Targeted versus Untargeted Strategies
Data Handling
Variable Selection
Data Modeling
Model Validation
Conclusions
References
Chapter 28. Analytical Methods and Biomarker Validation
Introduction
Discussion
Experimental Design and Execution
Biomarker Identification and Confirmation
Biomarker Validation
Conclusions
References
Index
- No. of pages: 488
- Language: English
- Edition: 1
- Published: May 20, 2013
- Imprint: Academic Press
- Hardback ISBN: 9780123944467
- eBook ISBN: 9780123947956
HI
Haleem J. Issaq
Haleem J. Issaq received his B.S. degree from the American College of Istanbul, Turkey, a M.S. degree from the Technion, Israel Institute of Technology, and a Ph.D. in analytical chemistry from Georgetown University in 1972. He was a Principal Scientist and Head of the Separation Technologies and Assay Development Group within the Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., located within the National Cancer Institute at Frederick, Maryland. His research interests include multidimensional separation of complex protein/peptide mixtures using liquid-phase-based separations (LC/LC, IEF/LC, and LC/CE), fast separation of estrogens, and use of HPLC/MS metabolomics for disease biomarker detection. He is the author or coauthor of over 350 scientific publications and the editor of A Century of Separation Science. He is the recipient of numerous awards, including Maryland Chemist of the Year.
Affiliations and expertise
Emeritus Scientist, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by The National Cancer Institute, Frederick, Maryland, USARead Proteomic and Metabolomic Approaches to Biomarker Discovery on ScienceDirect