Proteomic and metabolomic approaches to biomarker discovery /

Proteomic and metabolomic approaches to biomarker discovery /

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Bibliographic Details
Edition:Second edition.
Imprint:Amsterdam : Academic Press, 2019.
Description:1 online resource
Language:English
Subject:
Biochemical markers.
Proteomics -- Methodology.
Metabolism -- Regulation.
Electronic books.
Format: E-Resource Book
URL for this record:http://pi.lib.uchicago.edu/1001/cat/bib/11981979
Hidden Bibliographic Details
Other authors / contributors:Issaq, Haleem J., editor.
Veenstra, Timothy Daniel, 1966- editor.
ISBN:9780128186077
0128186070
9780128197882
0128197889
Notes:Previous edition: 2013.
Print version record.
Other form:Print version: 9780128186077
Table of Contents:
  • Contributors
  • Preface to the second edition
  • 1. Biomarker discovery: Study design and execution
  • 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
  • Acknowledgments
  • References
  • 2. Proteomic and mass spectrometry technologies for biomarker discovery
  • Introduction
  • Protein biomarker discovery and development pipeline
  • Proteomic samples
  • Protein identification using mass spectrometry
  • Posttranslational modifications as disease biomarkers
  • Protein quantification using mass spectrometry
  • Biomarker verification
  • Biomarker validation
  • Limitations of mass spectrometry for protein biomarker discovery
  • Conclusions and future outlook: Integrated biomarker discovery platform
  • References
  • 3. Tissue sample preparation for proteomic analysis
  • Introduction
  • Types of tissues available for MS-based proteomics
  • Tissue processing for LC-MS analysis
  • Extraction/solubilization buffers
  • Immunodepletion of abundant serum proteins from tissue homogenates
  • Concluding remarks
  • Acknowledgments
  • References
  • 4. Sample preparation in global metabolomics of biological fluids and tissues
  • Introduction
  • An ideal sample preparation method for global metabolomics?
  • Sample preparation methods for biofluids
  • Sample preparation methods for tissues
  • New trends in sample preparation for global metabolomics
  • Overview of sample preparation approaches for lipidomics
  • Quality control of sample preparation in global metabolomics
  • Conclusions and future perspective
  • Acknowledgment
  • References
  • 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
  • Update
  • References
  • 6. 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
  • 7. Current NMR strategies for biomarker discovery
  • Introduction: Why NMR?
  • Advancements in NMR hardware
  • Sample preparation for NMR analysis
  • One-dimensional NMR methods: 1 H, 13 C, 31 P
  • 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
  • 8. Gas chromatography/mass spectrometry-based metabonomics
  • Introduction
  • GC/MS in metabonomics
  • Strategies to address large-scale metabonomic investigations
  • Conclusion and future outlook
  • Update
  • References
  • 9. Liquid chromatographic methods combined with mass spectrometry in metabolomics
  • Introduction
  • Chromatographic methods for metabolite profiling
  • Ion mobility spectrometry combined with LC-MS
  • Detection
  • Quality control, data analysis, and biomarker detection
  • Metabolite identification and biomarker validation
  • Conclusions
  • References
  • Further reading
  • 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
  • Update
  • Acknowledgments
  • References
  • 11. Associating 2-DE and CPLLs for low-abundance protein discovery: A winning strategy
  • Historical recalls
  • Progressive evolution of 2-DE toward proteomics applications
  • Low-abundance proteins as a major target in proteomics
  • Enriching low-abundance proteins by the treatment of the initial sample
  • The discovery of low-abundance protein with 2-DE and its association with CPLLs enrichment
  • Toward the discovery of undetectable low-abundance proteins
  • Conclusion
  • References
  • 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-DIGF
  • Application of 2D-DIGE to biomarker discovery
  • Update
  • Conclusions
  • Acknowledgment
  • References
  • 13. Affinity-targeting schemes for protein biomarkers
  • Introduction
  • Conclusion
  • References
  • 14. Protein and metabolite identification
  • Protein identification
  • Metabolite identification in global metabolomics
  • Conclusion
  • References
  • 15. Quantitative proteomics in development of disease protein biomarkers
  • Introduction
  • Quantitative proteomic profiling for protein biomarker discovery
  • Targeted proteomic validation of biomarker candidates
  • Sample throughput in biomarker validation
  • Standardization
  • Public data repositories for assay development
  • Conclusion
  • References
  • 16. Mass spectrometry and NMR spectroscopy based quantitative metabolomics
  • Metabolomics
  • Mass spectrometry
  • NMR spectroscopy
  • Conclusions
  • References
  • 17. Top-down mass spectrometry for protein molecular diagnostics, structure analysis, and biomarker discovery
  • Introduction
  • Mass spectrometry hardware for top-down
  • Sample preparation and separations
  • Informatics
  • Current status
  • Concluding remarks
  • Acknowledgments
  • References
  • 18. Using data-independent mass spectrometry to extend detectable dynamic range without prior fractionation
  • Introduction
  • PAcIFIC and quantification
  • Proteome profiling with PAcIFIC
  • Conclusions
  • References
  • 19. Imaging mass spectrometry of intact biomolecules in tissue sections
  • Introduction
  • Matrix application
  • Protein analysis
  • Peptides and protein digests
  • Lipid analysis
  • Drug analysis
  • Three-dimensional imaging
  • High-speed imaging
  • Conclusions and perspectives
  • Acknowledgments
  • References
  • 20. Mass spectrometry-based approach for protein biomarker verification
  • 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
  • 21. Mass spectrometry metabolomic data handling for biomarker discovery
  • Metabolomics for biomarker discovery
  • Mass spectrometry-based metabolomics
  • Targeted vs. untargeted strategies
  • Data handling
  • Data modeling
  • Conclusion
  • References
  • 22. Analytical methods and biomarker validation
  • Introduction
  • Discussion
  • Experimental design and execution
  • Biomarker identification and confirmation
  • Biomarker validation
  • Conclusions
  • Update
  • References
  • 23. Multivariate analysis for metabolomics and proteomics data
  • Study 1. Cancer detection by proteomics
  • Study 2. Detection of heart disease by metabolomics
  • Conclusions
  • References
  • 24. Cell surface protein enrichment for biomarker and drug target discovery using mass spectrometry-based proteomics
  • Introduction
  • Cell surface proteomics in the context of biomarker discovery
  • Enrichment of cell surface proteins for bottom-up MS-based proteomics
  • Combined approaches for enrichment of cell surface protein
  • Concluding remarks
  • Acknowledgments
  • References
  • 25. Advances in lipidomics for cancer biomarker discovery
  • Introduction
  • Conclusion
  • References
  • 26. Mass spectrometry for the identification of protein biomarkers in urinary extracellular vesicles
  • Acknowledgments
  • References
  • 27. Designing clinical studies for biomarker discovery: The Design criteria
  • Introduction
  • Methodological aspects of biomarker identification studies: The Design criteria
  • Regulatory and ethical aspects
  • Conclusions
  • References
  • Index

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