Mass Spectrometry-Based Proteomics

This detailed volume explores contemporary techniques in mass spectrometry-based proteomics. After covering overall proteome coverage and the cellular surfaceome, the book delves into proximity-induced biotinylation, abduction of protein complexes in viral-like particles, and thermal proteome profiling, as well as protocols for identifying protein N-terminal acetylation, protein processing by proteases, protein N-glycosylation, and protein phosphorylation. The book also collects chapters on automated preparation of clinical samples, the analysis of formalin-fixed paraffin-embedded samples, protocols for the isolation of extracellular vesicles and for the monitoring of selected protein modifications in clinical samples, and, finally, structural proteomics. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, Mass Spectrometry-Based Proteomics serves as an ideal guide to its subject for both novices in the field of proteomics as well as specialists.

Includes cutting-edge techniques Provides step-by-step detail essential for reproducible results Contains key implementation advice from the experts

Contenu

1. Increasing the Overall Proteome Coverage by Combining Protein Digestion by Tryp-N and Trypsin.- Cell Surface Biotinylation Using Furan Crosslinking Chemistry.- Studying Cellular Dynamics Using Proximity-Dependent Biotinylation: Somatic Cell Reprogramming.- Virotrap: Trapping Protein Complexes in Virus-Like Particles.- Thermal Proteome Profiling for Drug Target Identification and Probing of Protein States.- Improved Coverage of the N-Terminome by Combining ChaFRADIC with Alternative Proteases.- Sensitive and High-Throughput Exploration of Protein N Termini by TMT-TAILS N-Terminomics.- The Global Acetylation Profiling Pipeline for Quick Assessment of Protein N-Acetyltransferase Specificity In Cellulo.- Systems-Wide Site-Specific Analysis of Glycoproteins.- Targeted Profiling of Protein Phosphorylation in Plants.- Automated Sample Preparation for Mass Spectrometry-Based Clinical Proteomics.- Proteomics-Based Analysis and Diagnosis of Formalin-Fixed Paraffin-Embedded Amyloidosis Samples.- A Robust and Clinically-Applicable Sample Preparation Protocol for Urinary Extracellular Vesicle Isolation Suitable for Mass Spectrometry-Based Proteomics.- Density-Based Fractionation of Cell Conditioned Medium to Prepare Proteomics Grade Extracellular Vesicles.- Mass Spectrometry-Based Analysis of Histone Post-Translational Modifications from Laser Microdissected Samples.- Phosphoproteomics after Guanidinium Thiocyanate Extraction of Tissue Biopsies.- Probing Antibody Structures by Hydrogen/Deuterium Exchange Mass Spectrometry.