Low-Abundance Proteome Discovery

Low-Abundance Proteome Discovery

State of the Art and Protocols

1st Edition - March 26, 2013

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  • Authors: Egisto Boschetti, Pier Giorgio Righetti
  • Paperback ISBN: 9780124017344
  • eBook ISBN: 9780124045965

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Description

Low-Abundance Proteome Discovery addresses the most critical challenge in biomarker discovery and progress: the identification of low-abundance proteins. The book describes an original strategy developed by the authors that permits the detection of protein species typically found in very low abundance and that may yield valuable clues to future discoveries. Known as combinatorial peptide ligand libraries, these new methodologies are one of the hottest topics related to the study of proteomics and have applications in medical diagnostics, food quality, and plant analysis. The book is written for university and industry scientists starting proteomic studies of complex matrices (e.g., biological fluids, biopsies, recalcitrant plant tissues, foodstuff, and beverage analysis), researchers doing wet chemistry, and graduate-level students in the areas of analytical and biochemistry, biology, and genetics.

Key Features

  • Covers methodologies for enhancing the visibility of low-abundance proteins which, until now, has been the biggest challenge in biomarker progress
  • Includes detailed protocols that address real-life needs in laboratory practice
  • Addresses all applications, including human disease, food and beverage safety, and the discovery of new proteins/peptides of importance in nutraceutics
  • Compiles the research and analytic protocols of the two scientists who are credited with the discovery of these landmark methodologies, also known as combinatorial peptide ligand libraries, for the identification of low-abundance proteins

Readership

Analytical chemists, biochemists, clinical chemists, biologists, including graduate-level students in these disciplines; genetic and biomedical researchers

Table of Contents

  • Acknowledgments

    Preface

    Biography

    Pier Giorgio Righetti

    Egisto Boschetti

    Abbreviations

    Trade Names

    Antiphon

    Chapter 1. Introducing Low-Abundance Species in Proteome Analysis

    1.1 The Proteomic Arena

    1.2 Low-Abundance Protein Definition and Their Tracking Interest

    1.3 Categories of Low-Abundance Proteins

    1.4 The Proposal for Low-Abundance Protein Access

    1.5 References

    Chapter 2. Chromatographic and Electrophoretic Prefractionation Tools in Proteome Analysis

    2.1 Introduction

    2.2 Prefractionation Tools in Proteome Analysis

    2.3 Sample Prefractionation via Different Electrophoretic Techniques

    2.4 Conclusions

    2.5 References

    Chapter 3. Current Low-Abundance Protein Access

    3.1 General Situation

    3.2 High-Abundance Protein Subtraction

    3.3 Enrichment of Low-Abundance, Post-translationally Modified Protein Groups

    3.4 Low-Abundance Protein Grouping by Common Interaction

    3.5 Importance and Limits of Classical Affinity-Enrichment Methods

    3.6 Integration of Low-Abundance Protein Access Methods

    3.7 References

    Chapter 4. Low-Abundance Protein Access by Combinatorial Peptide Libraries

    4.1 Combinatorial Chemistry

    4.2 Combinatorial Peptide Libraries

    4.3 Preparation of Solid-phase Combinatorial Peptide Ligand Libraries

    4.4 Use of Peptide Ligand Libraries as a Means of Reducing Protein Dynamic Range Concentration

    4.5 Peptide Ligand Library Properties in Protein Capturing

    4.6 Elution Mechanism Diversity and Complexity

    4.7 Selection of Elution Processes as a Function of Analytical Methods

    4.8 Towards a two-dimensional protein capture?

    4.9 References

    Chapter 5. Plant Proteomics and Food and Beverage Analysis via CPLL Capture

    5.1 Introducing Global Protein Analysis in Food

    5.2 Plant and Recalcitrant Tissues Proteomics

    5.3 Food and Beverages Proteomics: Examples and Potential Applications

    5.4 Conclusions

    5.5 References

    Chapter 6. Biomedical Involvements of Low-Abundance Proteins

    6.1 Introduction

    6.2 Biomarkers: Some Definitions and General Aspects

    6.3 Biomarker Discovery: A Gloomy Landscape

    6.4 Proteomics of Human Body Fluids

    6.5 Beyond Human Biological Fluids

    6.6 Red Blood Cell Proteomics

    6.7 Tissue Proteomics

    6.8 Low-Abundance Allergens Access

    6.9 Conclusions

    6.10 References

    Chapter 7. Other Applications of Combinatorial Peptide Libraries

    7.1 Screening for Affinity Ligand Selection

    7.2 Polishing out Protein Impurities from Pure Biologicals

    7.3 Interaction Studies

    7.4 Present Trends and Future Prospects of Combinatorial Peptide Libraries

    7.5 References

    Chapter 8. Detailed Methodologies and Protocols

    8.1 Preparation of Combinatorial Peptide Ligand Libraries

    8.2 Chemical Modification of Combinatorial Peptides (e.g., Succinylation)

    8.3 Preparation of Biological Extracts

    8.5 Alternative Methods for Protein Precipitation

    8.6 Beads Conditioning Prior to Use

    8.7 General Method for Protein Capture in Physiological Conditions

    8.8 Protein Sample Treatment at Low Ionic strength

    8.9 Protein Sample Treatment at Different pHs

    8.10 Protein extract treatment in the presence of lyotropic salts

    8.11 Protein Sample Treatment in the Presence of Surfactants

    8.12 Use of Two Complementary Peptide Libraries

    8.13 Plant Protein Enrichment

    8.14 Most Common Single-Elution Protocols

    8.15 Absolute Elution Protocols

    8.16 Fractionated (or Sequential) Elution Protocols

    8.17 Mild Elution Methods for Functional Studies

    8.17.2 Remarks and Recommendations

    8.18 Displacement Elution

    8.19 A Note of Caution on Elution Protocols

    8.20 On-bead Digestion

    8.21 Glycoprotein Enrichment

    8.22 Identification of Peptide Ligands by the Bead-Blot Method

    8.23 Determination of Binding Capacity by Frontal Analysis

    8.24 Reusing Combinatorial Ligand Library Beads?

    8.25 Monodimensional SDS-PAGE Prior to LC-MS/MS

    8.26 Two-dimensional Electrophoresis after Peptide Library Enrichment

    8.27 Immunoblot and Spot Identification

    8.28 2D-DIGE Following Peptide Library Enrichment

    8.29 References

    Polyphony

    Selected CPLL Bibliography

    Relevant Chronological Publications on Combinatorial Peptide Ligand Libraries Applied to Proteomics Investigations

    Index

Product details

  • No. of pages: 364
  • Language: English
  • Copyright: © Elsevier 2013
  • Published: March 26, 2013
  • Imprint: Elsevier
  • Paperback ISBN: 9780124017344
  • eBook ISBN: 9780124045965

About the Authors

Egisto Boschetti

Egisto Boschetti

Affiliations and Expertise

Scientific Consultant, Paris, France

Pier Giorgio Righetti

Pier Giorgio Righetti

Affiliations and Expertise

Miles Gloriosus Academy, Milano, Italy

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