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.
1. Cover image - p. iv 2. Title page - p. iv 3. Table of Contents - p. iv 4. Copyright - p. iv 5. Contributors - p. xiii 6. Preface - p. xiii 7. Chapter One: An Easy and Fast Protocol for Affinity Bead-Based Protein Enrichment and Storage of Proteome Samples - p. xviii 8. Chapter Two: Filter-Aided Sample Preparation: The Versatile and Efficient Method for Proteomic Analysis - p. 13 9. Chapter Three: An Overview of Advanced SILAC-Labeling Strategies for Quantitative Proteomics - p. 27 10. Chapter Four: Label-Free and Standard-Free Absolute Quantitative Proteomics Using the “Total Protein” and “Proteomic Ruler” Approaches - p. 47 11. Chapter Five: Separation of Two Distinct O-Glycoforms of Human IgA1 by Serial Lectin Chromatography Followed by Mass Spectrometry O-Glycan Analysis - p. 60 12. Chapter Six: Monitoring Protein Synthesis in Caenorhabditis elegans Using SILAC - p. 75 13. Chapter Seven: Identification of Novel Macropinocytosing Human Antibodies by Phage Display and High-Content Analysis - p. 89 14. Chapter Eight: Beyond the Natural Proteome: Nondegenerate Saturation Mutagenesis—Methodologies and Advantages - p. 110 15. Chapter Nine: WGCNA Application to Proteomic and Metabolomic Data Analysis - p. 133 16. Chapter Ten: A Protocol for Large-Scale Proteomic Analysis of Microdissected Formalin Fixed and Paraffin Embedded Tissue - p. 158 17. Chapter Eleven: Body Fluid Degradomics and Characterization of Basic N-Terminome - p. 176 18. Chapter Twelve: Reannotation of Genomes by Means of Proteomics Data - p. 199 19. Chapter Thirteen: Proteogenomics: Recycling Public Data to Improve Genome Annotations - p. 216 20. Chapter Fourteen: Targeted In-Depth Quantification of Signaling Using Label-Free Mass Spectrometry - p. 243 21. Chapter Fifteen: Biotin Switch Assays for Quantitation of Reversible Cysteine Oxidation - p. 268 22. Chapter Sixteen: Application of a Thioredoxin-Trapping Mutant for Analysis of the Cellular Nitrosoproteome - p. 284 23. Chapter Seventeen: Combining Click Chemistry-Based Proteomics With Dox-Inducible Gene Expression - p. 294 24. Chapter Eighteen: Analysis of the Proteome of Hair-Cell Stereocilia by Mass Spectrometry - p. 327 25. Chapter Nineteen: Proteomic Analysis of Metabolic Responses to Biofuels and Chemicals in Photosynthetic Cyanobacteria - p. 354 26. Chapter Twenty: Deep Profiling of Proteome and Phosphoproteome by Isobaric Labeling, Extensive Liquid Chromatography, and Mass Spectrometry - p. 376 27. Chapter Twenty-One: Glycoprotein Enrichment Analytical Techniques: Advantages and Disadvantages - p. 395 28. Chapter Twenty-Two: Quantitative Glycomics: A Combined Analytical and Bioinformatics Approach - p. 429 29. Author Index - p. 479 30. Subject Index - p. 517
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.
1. Cover image - p. iv 2. Title page - p. iv 3. Table of Contents - p. iv 4. Copyright - p. iv 5. Contributors - p. xiii 6. Preface - p. xiii 7. Chapter One: An Easy and Fast Protocol for Affinity Bead-Based Protein Enrichment and Storage of Proteome Samples - p. xviii 8. Chapter Two: Filter-Aided Sample Preparation: The Versatile and Efficient Method for Proteomic Analysis - p. 13 9. Chapter Three: An Overview of Advanced SILAC-Labeling Strategies for Quantitative Proteomics - p. 27 10. Chapter Four: Label-Free and Standard-Free Absolute Quantitative Proteomics Using the “Total Protein” and “Proteomic Ruler” Approaches - p. 47 11. Chapter Five: Separation of Two Distinct O-Glycoforms of Human IgA1 by Serial Lectin Chromatography Followed by Mass Spectrometry O-Glycan Analysis - p. 60 12. Chapter Six: Monitoring Protein Synthesis in Caenorhabditis elegans Using SILAC - p. 75 13. Chapter Seven: Identification of Novel Macropinocytosing Human Antibodies by Phage Display and High-Content Analysis - p. 89 14. Chapter Eight: Beyond the Natural Proteome: Nondegenerate Saturation Mutagenesis—Methodologies and Advantages - p. 110 15. Chapter Nine: WGCNA Application to Proteomic and Metabolomic Data Analysis - p. 133 16. Chapter Ten: A Protocol for Large-Scale Proteomic Analysis of Microdissected Formalin Fixed and Paraffin Embedded Tissue - p. 158 17. Chapter Eleven: Body Fluid Degradomics and Characterization of Basic N-Terminome - p. 176 18. Chapter Twelve: Reannotation of Genomes by Means of Proteomics Data - p. 199 19. Chapter Thirteen: Proteogenomics: Recycling Public Data to Improve Genome Annotations - p. 216 20. Chapter Fourteen: Targeted In-Depth Quantification of Signaling Using Label-Free Mass Spectrometry - p. 243 21. Chapter Fifteen: Biotin Switch Assays for Quantitation of Reversible Cysteine Oxidation - p. 268 22. Chapter Sixteen: Application of a Thioredoxin-Trapping Mutant for Analysis of the Cellular Nitrosoproteome - p. 284 23. Chapter Seventeen: Combining Click Chemistry-Based Proteomics With Dox-Inducible Gene Expression - p. 294 24. Chapter Eighteen: Analysis of the Proteome of Hair-Cell Stereocilia by Mass Spectrometry - p. 327 25. Chapter Nineteen: Proteomic Analysis of Metabolic Responses to Biofuels and Chemicals in Photosynthetic Cyanobacteria - p. 354 26. Chapter Twenty: Deep Profiling of Proteome and Phosphoproteome by Isobaric Labeling, Extensive Liquid Chromatography, and Mass Spectrometry - p. 376 27. Chapter Twenty-One: Glycoprotein Enrichment Analytical Techniques: Advantages and Disadvantages - p. 395 28. Chapter Twenty-Two: Quantitative Glycomics: A Combined Analytical and Bioinformatics Approach - p. 429 29. Author Index - p. 479 30. Subject Index - p. 517
