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.
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Table of Contents
Section I. Introduction1. Book introduction
2. MS Proteomic Overview
Section II. Sample Preparation
3. Sample preparation from mammalian cell lines
4. Sample preparation for proteomics and MS from clinical tissue
5. Sample preparation for proteomics and MS from biological fluids, e.g. serum/plasma from patient blood
6. Sample preparation for proteomics and MS from bacterial and fungal samples
7. Sample preparation for proteomics and MS from urine samples including exosome isolation
8. Sample preparation for proteomics and MS from animal samples
9. Subcellular fractionation methods for proteomic analysis
Section III. Protein Digestion
10. In gel digestion for mass spectrometry
11. In solution digestion for mass spectrometry
Section IV. MS Proteomic Analysis Protocols
12. Protocols for Label-free LC-MS/MS proteomic analysis
13. Protocols for TMT labelled LC-MS/MS analysis
14. Phosphorylation enrichment for phosphoproteomic analysis
15. Ubiquitination enrichment for ubiquitinome PTM analysis
16. Glycosylation enrichment and analysis
17. LC-MS for protein identification and PTM analysis (e.g. methylation)
