Proteomic and Metabolomic Approaches to Biomarker Discovery, Second Edition 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.
This second edition has been fully updated and revised to address recent advances in MS and NMR instrumentation, high-field NMR, proteomics and metabolomics for biomarker validation, clinical assays of biomarkers and clinical MS and NMR, identifying microRNAs and autoantibodies as biomarkers, MRM-MS assay development, top-down MS, glycosylation-based serum biomarkers, cell surface proteins in biomarker discovery, lipodomics for cancer biomarker discovery, and strategies to design studies to identify predictive biomarkers in cancer research.
1. Cover image - p. iv 2. Title page - p. iv 3. Table of Contents - p. iv 4. Copyright - p. iv 5. Contributors - p. xi 6. Preface to the second edition - p. xv 7. Chapter 1: Biomarker discovery: Study design and execution - p. xvi 8. Chapter 2: Proteomic and mass spectrometry technologies for biomarker discovery - p. 16 9. Chapter 3: Tissue sample preparation for proteomic analysis - p. 37 10. Chapter 4: Sample preparation in global metabolomics of biological fluids and tissues - p. 52 11. Chapter 5: Serum and plasma collection: Preanalytical variables and standard operating procedures in biomarker research - p. 83 12. Chapter 6: Sample depletion, fractionation, and enrichment for biomarker discovery - p. 94 13. Chapter 7: Current NMR strategies for biomarker discovery - p. 102 14. Chapter 8: Gas chromatography/mass spectrometry-based metabonomics - p. 131 15. Chapter 9: Liquid chromatographic methods combined with mass spectrometry in metabolomics - p. 147 16. Chapter 10: Capillary electrophoresis-mass spectrometry for proteomic and metabolic analysis - p. 169 17. Chapter 11: Associating 2-DE and CPLLs for low-abundance protein discovery: A winning strategy - p. 182 18. Chapter 12: Two-dimensional difference in gel electrophoresis for biomarker discovery - p. 207 19. Chapter 13: Affinity-targeting schemes for protein biomarkers - p. 214 20. Chapter 14: Protein and metabolite identification - p. 245 21. Chapter 15: Quantitative proteomics in development of disease protein biomarkers - p. 260 22. Chapter 16: Mass spectrometry and NMR spectroscopy based quantitative metabolomics - p. 288 23. Chapter 17: Top-down mass spectrometry for protein molecular diagnostics, structure analysis, and biomarker discovery - p. 311 24. Chapter 18: Using data-independent mass spectrometry to extend detectable dynamic range without prior fractionation - p. 326 25. Chapter 19: Imaging mass spectrometry of intact biomolecules in tissue sections - p. 337 26. Chapter 20: Mass spectrometry-based approach for protein biomarker verification - p. 352 27. Chapter 21: Mass spectrometry metabolomic data handling for biomarker discovery - p. 368 28. Chapter 22: Analytical methods and biomarker validation - p. 388 29. Chapter 23: Multivariate analysis for metabolomics and proteomics data - p. 393 30. Chapter 24: Cell surface protein enrichment for biomarker and drug target discovery using mass spectrometry-based proteomics - p. 407 31. Chapter 25: Advances in lipidomics for cancer biomarker discovery - p. 420 32. Chapter 26: Mass spectrometry for the identification of protein biomarkers in urinary extracellular vesicles - p. 436 33. Chapter 27: Designing clinical studies for biomarker discovery: The Design criteria - p. 440 34. Index - p. 467
Proteomic and Metabolomic Approaches to Biomarker Discovery, Second Edition 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.
This second edition has been fully updated and revised to address recent advances in MS and NMR instrumentation, high-field NMR, proteomics and metabolomics for biomarker validation, clinical assays of biomarkers and clinical MS and NMR, identifying microRNAs and autoantibodies as biomarkers, MRM-MS assay development, top-down MS, glycosylation-based serum biomarkers, cell surface proteins in biomarker discovery, lipodomics for cancer biomarker discovery, and strategies to design studies to identify predictive biomarkers in cancer research.
1. Cover image - p. iv 2. Title page - p. iv 3. Table of Contents - p. iv 4. Copyright - p. iv 5. Contributors - p. xi 6. Preface to the second edition - p. xv 7. Chapter 1: Biomarker discovery: Study design and execution - p. xvi 8. Chapter 2: Proteomic and mass spectrometry technologies for biomarker discovery - p. 16 9. Chapter 3: Tissue sample preparation for proteomic analysis - p. 37 10. Chapter 4: Sample preparation in global metabolomics of biological fluids and tissues - p. 52 11. Chapter 5: Serum and plasma collection: Preanalytical variables and standard operating procedures in biomarker research - p. 83 12. Chapter 6: Sample depletion, fractionation, and enrichment for biomarker discovery - p. 94 13. Chapter 7: Current NMR strategies for biomarker discovery - p. 102 14. Chapter 8: Gas chromatography/mass spectrometry-based metabonomics - p. 131 15. Chapter 9: Liquid chromatographic methods combined with mass spectrometry in metabolomics - p. 147 16. Chapter 10: Capillary electrophoresis-mass spectrometry for proteomic and metabolic analysis - p. 169 17. Chapter 11: Associating 2-DE and CPLLs for low-abundance protein discovery: A winning strategy - p. 182 18. Chapter 12: Two-dimensional difference in gel electrophoresis for biomarker discovery - p. 207 19. Chapter 13: Affinity-targeting schemes for protein biomarkers - p. 214 20. Chapter 14: Protein and metabolite identification - p. 245 21. Chapter 15: Quantitative proteomics in development of disease protein biomarkers - p. 260 22. Chapter 16: Mass spectrometry and NMR spectroscopy based quantitative metabolomics - p. 288 23. Chapter 17: Top-down mass spectrometry for protein molecular diagnostics, structure analysis, and biomarker discovery - p. 311 24. Chapter 18: Using data-independent mass spectrometry to extend detectable dynamic range without prior fractionation - p. 326 25. Chapter 19: Imaging mass spectrometry of intact biomolecules in tissue sections - p. 337 26. Chapter 20: Mass spectrometry-based approach for protein biomarker verification - p. 352 27. Chapter 21: Mass spectrometry metabolomic data handling for biomarker discovery - p. 368 28. Chapter 22: Analytical methods and biomarker validation - p. 388 29. Chapter 23: Multivariate analysis for metabolomics and proteomics data - p. 393 30. Chapter 24: Cell surface protein enrichment for biomarker and drug target discovery using mass spectrometry-based proteomics - p. 407 31. Chapter 25: Advances in lipidomics for cancer biomarker discovery - p. 420 32. Chapter 26: Mass spectrometry for the identification of protein biomarkers in urinary extracellular vesicles - p. 436 33. Chapter 27: Designing clinical studies for biomarker discovery: The Design criteria - p. 440 34. Index - p. 467
