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Proteomics in Biology, Part A

1st Edition - January 19, 2017

Editor: Arun K. Shukla

Hardback ISBN:

9 7 8 - 0 - 1 2 - 8 0 9 7 4 2 - 7

eBook ISBN:

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.

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