Proteomics Mass Spectrometry Methods: Sample Preparation, Protein Digestion, and Research Protocols shares best practices collected across key laboratories and core facilities, taking the reader through key tactics for executing the most usual mass spectrometry experiments. Sections review research making use of MS proteomics experiments, focus on critical sample preparation, cover mammalian cell lines and samples from clinical tissue and biological fluids, discuss subcellular fractionation, provide methods for protein digestion both for in gel and in solution, and delve into key MS proteomics analysis protocols, including label-free LC-MS, TMT and iTRAQ labelled LC-MS, phosphorylation enrichment, ubiquination enrichment, and more. This book is the perfect lab manual for research teams or for use as a new staff training material. Core facility managers may also find it useful for sharing best practices with their staff and researchers.
1. Chapter 1 Book introduction - p. 3 2. Chapter 2 Introduction to sample preparation for proteomics and mass spectrometry - p. 7 3. Chapter 3 Sample preparation for proteomics and mass spectrometry from mammalian cell lines - p. 35 4. Chapter 4 Sample preparation for proteomics and mass spectrometry from clinical tissue - p. 55 5. Chapter 5 Sample preparation for proteomics and mass spectrometry from patient biological fluids - p. 79 6. Chapter 6 Preparation of bacterial and fungal samples for proteomic analysis - p. 87 7. Chapter 7 Urinary extracellular vesicles isolated by hydrostatic filtration dialysis without Tamm–Horsfall protein interference for Mass Spectrometry analysis - p. 101 8. Chapter 8 Sample preparation for proteomics and mass spectrometry from animal samples - p. 117 9. Chapter 9 In-gel tryptic digestion approaches for protein and proteome characterization - p. 127 10. Chapter 10 Protocols for label-free LC-MS/MS proteomic analysis - p. 141 11. Chapter 11 Profiling of the phosphoproteome using tandem mass tag labeling - p. 163 12. Chapter 12 Phosphopeptide enrichment and post translational modification characterization using LC-MS/MS - p. 173 13. Chapter 13 Ubiquitin diGly peptide enrichment and LC-MS/MS analysis to characterize the ubiquitinated proteome of mammalian cells - p. 189 14. Chapter 14 Liquid chromatography mass spectrometry–based proteomics: Global cell proteome profile - p. 199 15. Index - p. 219
Proteomics Mass Spectrometry Methods: Sample Preparation, Protein Digestion, and Research Protocols shares best practices collected across key laboratories and core facilities, taking the reader through key tactics for executing the most usual mass spectrometry experiments. Sections review research making use of MS proteomics experiments, focus on critical sample preparation, cover mammalian cell lines and samples from clinical tissue and biological fluids, discuss subcellular fractionation, provide methods for protein digestion both for in gel and in solution, and delve into key MS proteomics analysis protocols, including label-free LC-MS, TMT and iTRAQ labelled LC-MS, phosphorylation enrichment, ubiquination enrichment, and more. This book is the perfect lab manual for research teams or for use as a new staff training material. Core facility managers may also find it useful for sharing best practices with their staff and researchers.
1. Chapter 1 Book introduction - p. 3 2. Chapter 2 Introduction to sample preparation for proteomics and mass spectrometry - p. 7 3. Chapter 3 Sample preparation for proteomics and mass spectrometry from mammalian cell lines - p. 35 4. Chapter 4 Sample preparation for proteomics and mass spectrometry from clinical tissue - p. 55 5. Chapter 5 Sample preparation for proteomics and mass spectrometry from patient biological fluids - p. 79 6. Chapter 6 Preparation of bacterial and fungal samples for proteomic analysis - p. 87 7. Chapter 7 Urinary extracellular vesicles isolated by hydrostatic filtration dialysis without Tamm–Horsfall protein interference for Mass Spectrometry analysis - p. 101 8. Chapter 8 Sample preparation for proteomics and mass spectrometry from animal samples - p. 117 9. Chapter 9 In-gel tryptic digestion approaches for protein and proteome characterization - p. 127 10. Chapter 10 Protocols for label-free LC-MS/MS proteomic analysis - p. 141 11. Chapter 11 Profiling of the phosphoproteome using tandem mass tag labeling - p. 163 12. Chapter 12 Phosphopeptide enrichment and post translational modification characterization using LC-MS/MS - p. 173 13. Chapter 13 Ubiquitin diGly peptide enrichment and LC-MS/MS analysis to characterize the ubiquitinated proteome of mammalian cells - p. 189 14. Chapter 14 Liquid chromatography mass spectrometry–based proteomics: Global cell proteome profile - p. 199 15. Index - p. 219
