Mass Spectrometry-Based Proteomics

ISBN-13: 9781071634561 / Angielski / Twarda / 2023

Opis

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.

Spis treści

1. Increasing the Overall Proteome Coverage by Combining Protein Digestion by Tryp-N and Trypsin

            Jade I. Hawksworth, Lode Denolf, Evy Timmerman, and Kris Gevaert

 

2. Cell Surface Biotinylation Using Furan Crosslinking Chemistry

            Esperanza Fernandez, Laia Miret-Casals, Annemieke Madder, and Kris Gevaert

 

3. Studying Cellular Dynamics Using Proximity-Dependent Biotinylation: Somatic Cell Reprogramming

            Reuben Samson, Francesco Zangari, and Anne-Claude Gingras

 

4. Virotrap: Trapping Protein Complexes in Virus-Like Particles

            George D. Moschonas, Margaux De Meyer, Delphine De Sutter, Evy Timmerman, Petra Van Damme, and Sven Eyckerman

 

5. Thermal Proteome Profiling for Drug Target Identification and Probing of Protein States

            Patricia Sauer and Marcus Bantscheff

 

6. Improved Coverage of the N-Terminome by Combining ChaFRADIC with Alternative Proteases

            Xuehui Jiang, Ying Lao, Victor Spicer, and René P. Zahedi

 

7. Sensitive and High-Throughput Exploration of Protein N Termini by TMT-TAILS N-Terminomics

            Konstantinos Kalogeropoulos, Louise Bundgaard, and Ulrich auf dem Keller

 

8. The Global Acetylation Profiling Pipeline for Quick Assessment of Protein N-Acetyltransferase Specificity In Cellulo

            Thierry Meinnel, Jean-Baptiste Boyer, and Carmela Giglione

 

9. Systems-Wide Site-Specific Analysis of Glycoproteins

            Kathirvel Alagesan and Emmanuelle Charpentier

 

10. Targeted Profiling of Protein Phosphorylation in Plants

            Xiangyu Xu, Kris Gevaert, Ive De Smet, and Lam Dai Vu

 

11. Automated Sample Preparation for Mass Spectrometry-Based Clinical Proteomics

            Torsten Müller, Mauro A. Cremonini, Georg Kliewer, and Jeroen Krijgsveld

 

12. Proteomics-Based Analysis and Diagnosis of Formalin-Fixed Paraffin-Embedded Amyloidosis Samples

            Delphi Van Haver, Amélie Dendooven, and Francis Impens

 

13. A Robust and Clinically-Applicable Sample Preparation Protocol for Urinary Extracellular Vesicle Isolation Suitable for Mass Spectrometry-Based Proteomics

            Leyla A. Erozenci, Irene V. Bijnsdorp, Sander R. Piersma, and Connie R. Jimenez

 

14. Density-Based Fractionation of Cell Conditioned Medium to Prepare Proteomics Grade Extracellular Vesicles

            Quentin Roux, Sarah Deville, and An Hendrix

 

15. Mass Spectrometry-Based Analysis of Histone Post-Translational Modifications from Laser Microdissected Samples

            Roberta Noberini and Tiziana Bonaldi

 

16. Phosphoproteomics after Guanidinium Thiocyanate Extraction of Tissue Biopsies

            Frank Rolfs, Richard R. de Goeij-de Haas, Jaco C. Knol, Sander R. Piersma, and Connie R. Jimenez

 

17. Probing Antibody Structures by Hydrogen/Deuterium Exchange Mass Spectrometry

            Zuzana Kalaninová, Lukáš Fojtík, Josef Chmelík, Petr Novák, Michael Volný, and Petr Man