
Proteomics in Biology, Part B
Description
Key Features
- Continues the legacy of this premier serial with quality chapters that focus on proteomics
- Contains contributions from leading authorities
Readership
Table of Contents
Chapter One: Protein Cysteinyl-S-Nitrosylation: Analysis and Quantification
- Abstract
- 1 Introduction
- 2 SNOFlo Methodology
- 3 Applications
Chapter Two: Quantitative Proteomics of the E. coli Membranome
- Abstract
- 1 Introduction—Pipeline Overview
- 2 Sample Preparation
- 3 Peptide/Protein Identification
- 4 Quantification
- 5 Functional Annotation
- 6 Conclusion
- Acknowledgments
Chapter Three: Comparative Analysis and Validation of Different Steps in Glycomics Studies
- Abstract
- 1 Introduction
- 2 Experimental Design and Randomization
- 3 Sample Preparation for UPLC N-Glycan Analysis
- 4 Robustness of the Sample Preparation Method
- 5 Analysis of Sources of Variation
- 6 Method Validation (Between-Day and Between-Analyst Variation)
- 7 UPLC Analysis of 2-AB-Labeled N-Glycans
- 8 Data Analysis and Quality Control
- 9 Summary and Conclusions
- Acknowledgments
Chapter Four: Analysis of Translocation-Competent Secretory Proteins by HDX-MS
- Abstract
- 1 Introduction
- 2 Preparation of Polypeptides
- 3 Isotope Labeling
- 4 Mass Spectrometric Analysis
- 5 Data Visualization and Interpretation
- 6 Identifying Statistically Significant Conformational Differences in Comparative Local HDX-MS
- 7 Conclusions
- Acknowledgments
Chapter Five: Site-Specific Quantification of Lysine Acetylation Using Isotopic Labeling
- Abstract
- 1 Introduction
- 2 Principle of Site-Specific Quantification of Lysine Acetylation Using Isotopic Labeling
- 3 Experimental Procedures
- 4 Conclusion
Chapter Six: Posttranslational Modifications and Plant–Environment Interaction
- Abstract
- 1 Introduction
- 2 Phosphorylation-Dependent Signal Transduction
- 3 Glycosylation and Protein Transport
- 4 Ubiquitination and Sumoylation-Dependent Protein Regulation
- 5 Role of Oxidative Modifications in Energy Production
- 6 Acetylation and Plant Immune Response
- 7 Posttranslational Modifications and Protein–Protein Interaction
- 8 Conclusion
Chapter Seven: Identification of Posttranslational Modifications of Endogenous Chromatin Proteins From Testicular Cells by Mass Spectrometry
- Abstract
- 1 Introduction
- 2 Isolation of Different Stages of Rat Testicular Germ Cells
- 3 Extraction of Nuclear Basic Proteins
- 4 Purification of Chromatin Proteins by RP-HPLC
- 5 Mass Spectrometry Analysis
- 6 Future Perspectives and Challenges
- 7 Biological Implications in Spermatogenesis
- Acknowledgments
Chapter Eight: Quantitative Analysis of Yeast Checkpoint Protein Kinase Activity by Combined Mass Spectrometry Enzyme Assays
- Abstract
- 1 Introduction
- 2 Established Methods to Monitor Rad53 Activation
- 3 A Direct Quantitative Immunoprecipitation Kinase Activity Assay for Endogenous Rad53
- 4 Mass Spectrometric Analysis of Rad53 Autophosphorylation
- 5 Conclusions
Chapter Nine: Retrieving Quantitative Information of Histone PTMs by Mass Spectrometry
- Abstract
- 1 Introduction
- 2 MS-Based Proteomics
- 3 Analysis of Histone Modifications: Methods and Strategies
- 4 Clinical Applications
- 5 Conclusion
Chapter Ten: Evaluating Exosome Protein Content Changes Induced by Virus Activity Using SILAC Labeling and LC-MS/MS
- Abstract
- 1 Introduction
- 2 Experimental Design
- 3 Detailed Protocol
- 4 Conclusions
Chapter Eleven: Exoproteomics of Pathogens: Analysis of Toxins and Other Virulence Factors by Proteomics
- Abstract
- 1 Introduction
- 2 Exoproteome Sample Preparation and Fractionation
- 3 Shotgun Mass Spectrometry for Discovery of Toxins and Other Virulence Factors
- 4 Data Interpretation
- 5 Examples of Specific Applications
- 6 Conclusion
Chapter Twelve: Integrated and Quantitative Proteomics of Human Tumors
- Abstract
- 1 Introduction
- 2 Equipment, Material, and Buffers
- 3 Wet Lab Protocol
- 4 Dry Lab Protocol
- 5 An Example
- 6 Conclusion
- Acknowledgments
Chapter Thirteen: Mass Spectrometry-Based Analysis for the Discovery and Validation of Potential Colorectal Cancer Stool Biomarkers
- Abstract
- 1 Introduction
- 2 Proteomics: From Discovery to Translation
- 3 Sample Preparation
- 4 Proteomic Discovery Protocols
- 5 Protein Quantitation Protocols
- 6 Future Directions
Chapter Fourteen: Mass Spectrometry-Based Methodology for Identification of Native Histone Variant Modifications From Mammalian Tissues and Solid Tumors
- Abstract
- 1 Introduction
- 2 Mass Spectrometry-Based Methods Overview
- 3 Protocol
- 4 Notes
- 5 Concluding Remarks
- Acknowledgments
Chapter Fifteen: Drug Target Identification Using an iTRAQ-Based Quantitative Chemical Proteomics Approach—Based on a Target Profiling Study of Andrographolide
- Abstract
- 1 Introduction and General Principles
- 2 Materials, Equipment, and Solutions
- 3 Protocol
- 4 Discussion
- Acknowledgments
Chapter Sixteen: A Super-SILAC Strategy for the Accurate and Multiplexed Profiling of Histone Posttranslational Modifications
- Abstract
- 1 Introduction
- 2 Overview of the Method
- 3 Material
- 4 Methods
- 5 Conclusions
- Acknowledgments
Chapter Seventeen: A Comparison of Two-Hybrid Approaches for Detecting Protein–Protein Interactions
- Abstract
- 1 Introduction
- 2 The Bacterial Two-Hybrid System
- 3 The Yeast Two-Hybrid System
- 4 Comparison of Yeast and Bacterial Two-Hybrid Methods
- 5 Conclusion
Chapter Eighteen: Recent Achievements in Characterizing the Histone Code and Approaches to Integrating Epigenomics and Systems Biology
- Abstract
- 1 Introduction
- 2 Sample Preparation
- 3 MS-Based Strategies for Histone Analysis
- 4 Future Perspective/Outlook
- Acknowledgments
Chapter Nineteen: Rapid Proteomics to Prospect and Validate Novel Bacterial Metabolism Induced by Environmental Burden
- Abstract
- 1 Introduction
- 2 Method Summary
- 3 Stable Isotope Dimethyl-Labeling Protocol
- 4 Applications
- 5 Conclusion
- Acknowledgments
Chapter Twenty: Quantitation of Human Metallothionein Isoforms in Cells, Tissues, and Cerebrospinal Fluid by Mass Spectrometry
- Abstract
- 1 Introduction
- 2 Methodology
- 3 Conclusions
- Acknowledgments
Chapter Twenty-One: A Cautionary Tale on the Inclusion of Variable Posttranslational Modifications in Database-Dependent Searches of Mass Spectrometry Data
- Abstract
- 1 Introduction
- 2 Scores and Thresholds
- 3 The Power of Calculating False Discovery Rates
- 4 The Advantages and Disadvantages of Including Some Common Posttranslational Modifications as Variable Modifications in Database-Dependent Searches
- 5 The Special Case of the GlyGly Modification
- 6 Conclusions
- Acknowledgments
Chapter Twenty-Two: Kinase Assay-Linked Phosphoproteomics: Discovery of Direct Kinase Substrates
- Abstract
- 1 Introduction
- 2 Overview of Kinase Substrate Identification Methods
- 3 Kinase Assay-Linked Phosphoproteomics Approach
- 4 Conclusions
- 5 Materials
- Acknowledgments
Product details
- No. of pages: 536
- Language: English
- Copyright: © Academic Press 2017
- Published: January 27, 2017
- Imprint: Academic Press
- eBook ISBN: 9780128105351
- Hardcover ISBN: 9780128097434
About the Serial Volume Editor
Arun K. Shukla
