Proteomic and Metabolomic Approaches to Biomarker Discovery - 1st Edition - ISBN: 9780123944467, 9780123947956

Proteomic and Metabolomic Approaches to Biomarker Discovery

1st Edition

Editors: Haleem J Issaq Timothy D. Veenstra
eBook ISBN: 9780123947956
Hardcover ISBN: 9780123944467
Imprint: Academic Press
Published Date: 18th June 2013
Page Count: 488
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Description

Proteomic 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.

Key Features

  • 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

Readership

Biochemists, analytical chemists, bioanalytical chemists, biologists, medical technicians, clinical technicians, researchers in pharmaceuticals, graduate students and all interested in the field of biomarkers research.

Table of Contents

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

Details

No. of pages:
488
Language:
English
Copyright:
© Academic Press 2013
Published:
Imprint:
Academic Press
eBook ISBN:
9780123947956
Hardcover ISBN:
9780123944467

About the Editor

Haleem J Issaq

Affiliations and Expertise

Ph.D., Laboratory of Proteomics and Analytical Technologies, SAIC/Frederick National Cancer Institute at Frederick, Frederick, MD, USA.

Timothy D. Veenstra

Affiliations and Expertise

Ph.D., Mass Spectrometry Center and Laboratory of Proteomics and Analytical Technologies, SAIC/Frederick National Cancer Institute at Frederick, Frederick, MD, USA.

Reviews

"The book is primarily aimed at researchers with significant expertise in proteomic or metabolomic technologies with an interest in pursuing biomarker discovery studies. The chapters are well written, informative, and provide insight into various steps from sample acquisition to data analysis. The book is an excellent starting point for anyone interested in this field."--Analytical and Bioanalytical Chemistry (2014) 406
"Researchers in various medical and biological specialties focus mostly on preparing samples for proteomic and metabolomic studies, rather than on using the imaging equipment."--Reference and Research Book News, August 2013