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Proteomics in Biology, Part A
1st Edition - January 19, 2017
Editor: Arun K. Shukla
Hardback ISBN:9780128097427
9 7 8 - 0 - 1 2 - 8 0 9 7 4 2 - 7
eBook ISBN:9780128105344
9 7 8 - 0 - 1 2 - 8 1 0 5 3 4 - 4
Proteomics in Biology Part A, the latest volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the… Read more
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Proteomics in Biology Part A, the latest volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field, and a focus on proteomics for this updated volume.
Continues the legacy of this premier serial with quality chapters that focus on proteomics
Contains contributions from leading authorities
Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists
Preface
Chapter One: An Easy and Fast Protocol for Affinity Bead-Based Protein Enrichment and Storage of Proteome Samples
Abstract
1 Introduction
2 StrataClean Beads for Protein Enrichment
3 General Protocol for the Use of StrataClean Beads in Proteomics
4 Application of StrataClean Beads in Protein Sample Preparation and Life Science Research
5 Protocol Variations
6 Conclusions
Chapter Two: Filter-Aided Sample Preparation: The Versatile and Efficient Method for Proteomic Analysis
Abstract
1 Introduction
2 The FASP Procedures
3 Filter-Aided Sample Preparation Protocols
Acknowledgments
Chapter Three: An Overview of Advanced SILAC-Labeling Strategies for Quantitative Proteomics
Abstract
1 Introduction
2 Dual Labeling to Exclude Unlabeled Proteins
3 Subsaturating Labeling
4 5-Plexed SILAC Labeling
5 Conclusion
Chapter Four: Label-Free and Standard-Free Absolute Quantitative Proteomics Using the “Total Protein” and “Proteomic Ruler” Approaches
Abstract
1 Introduction
2 TPA: For Determination of Protein Contents and Concentrations
3 Cell Size and Protein Copy Numbers Can Be Assessed by the Proteomic Ruler
4 Protein Concentrations and Copy Numbers Provide Different Layers of Information
5 Consistency of TPA Values With Biochemical Data
6 Normalization and Comparison of Datasets Using DJ-1/PARK7 Titer
7 Limitations
Acknowledgments
Chapter Five: Separation of Two Distinct O-Glycoforms of Human IgA1 by Serial Lectin Chromatography Followed by Mass Spectrometry O-Glycan Analysis
Abstract
1 Introduction
2 Methodology
3 Discussion
Acknowledgment
Chapter Six: Monitoring Protein Synthesis in Caenorhabditis elegans Using SILAC
Abstract
1 Introduction
2 Principle of SILAC-Based Measurement of Protein Synthesis in C. elegans
3 Experimental Procedures
4 Conclusion
Acknowledgment
Chapter Seven: Identification of Novel Macropinocytosing Human Antibodies by Phage Display and High-Content Analysis
Abstract
1 Introduction
2 HT-HCA Screening of Macropinocytic Antibodies: Overview of the Strategy and Method
3 HT-HCA Screening Protocol for Macropinocytic Phage Antibodies
4 Conclusion
Acknowledgments
Chapter Eight: Beyond the Natural Proteome: Nondegenerate Saturation Mutagenesis—Methodologies and Advantages
Abstract
1 Introduction
2 Advantages of Nondegenerate Saturation
3 Saturation Mutagenesis Methods
4 Screening the Library: Methods, Library Size, and the Importance of Diversity
5 Conclusions
Acknowledgments
Chapter Nine: WGCNA Application to Proteomic and Metabolomic Data Analysis
Abstract
1 Introduction
2 Overview of WGCNA Protocol
3 Application in Proteomic Analysis
4 Application in Metabolomics Analysis
5 Conclusions
Acknowledgments
Data Availability
Chapter Ten: A Protocol for Large-Scale Proteomic Analysis of Microdissected Formalin Fixed and Paraffin Embedded Tissue
Abstract
1 Introduction
2 FFPE–FASP–SAX Protocol
Acknowledgments
Chapter Eleven: Body Fluid Degradomics and Characterization of Basic N-Terminome
Abstract
1 Introduction
2 N-Terminal Enrichment Strategies
3 Body Fluid Degradomics by iTRAQ-TAILS
4 Validation by Targeted Proteomics and Establishment of Biomarker Assays
5 Conclusions
Acknowledgments
Chapter Twelve: Reannotation of Genomes by Means of Proteomics Data
Abstract
1 Introduction
2 Bacterial Proteogenomics: The Methods
3 General Protocol
4 Conclusion
Chapter Thirteen: Proteogenomics: Recycling Public Data to Improve Genome Annotations
Abstract
1 Introduction
2 Data
3 Databases
4 Peptide and Protein Identification
5 Proteogenomics Toolkits
6 Sequence Validation
7 Limitations
8 Concluding Remarks
Chapter Fourteen: Targeted In-Depth Quantification of Signaling Using Label-Free Mass Spectrometry
Abstract
1 Introduction
2 Phosphoproteomic Analysis as a Means to Quantify Cell Signaling
3 Overview of Methodologies for Phosphoproteomics
4 The Concepts of TIQUAS
5 Obtaining Biological Information From Phosphoproteomics Datasets
6 Conclusions
Chapter Fifteen: Biotin Switch Assays for Quantitation of Reversible Cysteine Oxidation
Abstract
1 Introduction
2 Chemicals
3 Method
4 Application
5 Conclusion
Chapter Sixteen: Application of a Thioredoxin-Trapping Mutant for Analysis of the Cellular Nitrosoproteome
Abstract
1 Introduction
2 Materials
3 Methods
4 Concluding Remarks
Acknowledgments
Chapter Seventeen: Combining Click Chemistry-Based Proteomics With Dox-Inducible Gene Expression
Abstract
1 Background
2 Combined Experimental Strategy
3 Application and Modification
4 Conclusion
Acknowledgments
Chapter Eighteen: Analysis of the Proteome of Hair-Cell Stereocilia by Mass Spectrometry
Abstract
1 Introduction
2 Isolation of Hair Bundles
3 Shotgun Mass Spectrometry
4 Targeted Mass Spectrometry
5 Summary
Acknowledgments
Chapter Nineteen: Proteomic Analysis of Metabolic Responses to Biofuels and Chemicals in Photosynthetic Cyanobacteria
Abstract
1 Introduction
2 Current Proteomics Methods Used in Analyzing Metabolic Responses
3 Metabolic Responses of Cyanobacteria to Biofuels Revealed by Proteomics
4 Metabolic Responses to Chemicals Revealed by Proteomics in Cyanobacteria
5 Conclusions
Acknowledgments
Chapter Twenty: Deep Profiling of Proteome and Phosphoproteome by Isobaric Labeling, Extensive Liquid Chromatography, and Mass Spectrometry
Abstract
1 Introduction
2 Sample Preparation by Harvesting Cells and Tissues
3 Protein Extraction, Quality Control Western Blotting, In-Solution Digestion, and Peptide Purification
4 TMT Labeling of Peptides
5 Offline Basic pH RPLC Fractionation
6 TiO2 Phosphopeptide Enrichment
7 Acidic pH RPLC-MS/MS Analysis
8 MS Data Analysis
9 Proteomics Results and Selected Validation
10 Conclusions and Discussion
Acknowledgments
Chapter Twenty-One: Glycoprotein Enrichment Analytical Techniques: Advantages and Disadvantages
Abstract
1 Proteomics: Posttranslational Modifications
2 Challenges Associated With Glycoprotein Analysis
3 Enrichment Techniques of Glycopeptides
4 High-Performance Liquid Chromatography in Proteomics and Glycoproteomics
5 Ion Mobility-Mass Spectrometry
6 Capillary Electrophoresis
7 Characterization of Intact Glycopeptides
8 Characterization of Intact Glycoproteins
9 Software Tools for MS/MS-Based Glycopeptide Characterization
10 Concluding Remarks and Future Directions
Acknowledgments
Chapter Twenty-Two: Quantitative Glycomics: A Combined Analytical and Bioinformatics Approach
Abstract
1 Protein Glycosylation
2 Sample Handling in Glycomics
3 Quantitative Glycomics Platforms
Acknowledgments
Author Index
Subject Index
No. of pages: 548
Language: English
Published: January 19, 2017
Imprint: Academic Press
Hardback ISBN: 9780128097427
eBook ISBN: 9780128105344
AS
Arun K. Shukla
Dr. Arun K. Shukla is a world leader in the field of GPCR biology and he is currently a Professor in the Department of Biological Sciences and Bioengineering at the Institute of Technology, Kanpur in India. Dr. Shukla’s research program is focused on understanding the structure, function and regulation of G protein-coupled receptors with a long-term of designing novel therapeutics with minimized side-effects.