Shotgun Proteomics, 1st ed. 2021 Methods and Protocols Methods in Molecular Biology Series, Vol. 2259

This edition details a collection of specific shotgun proteomics-based laboratory techniques and applications developed in leading laboratories and proteomics units worldwide. Chapters cover a broad range of topics covering, shotgun proteomics of extracellular vesicles and subcellular structures, shotgun proteomics in non-model organisms, clinical proteomics, food proteomics, analysis of post-translational modifications and protein complexes, and data processing and storage. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Shotgun Proteomics: Methods and Protocols aims to be an up-to-date guide for researchers seeking to understand the proteome of any given biological sample.

Part I: Shotgun Proteomics of Extracellular Vesicles and Subcellular Structures

1. Mesenchymal Stem Cell - Derived Extracellular Vesicles Isolation and their Protein Cargo Characterisation

Miriam Morente-López, Juan A. Fafián-Labora, Mónica Carrera, Francisco J. de Toro, Concha Gil, Jesús Mateos, and María C. Arufe

2. Clinical Proteomics for the Analysis of Circulating Extracellular Vesicles

Maria N. Barrachinaand Ángel García

3. Utilization of Laser Capture Microdissection Coupled to Mass Spectrometry to Uncover the Proteome of Cellular Protrusions

Ana Gordonand Karine Gousset

Part II: Shotgun Proteomics of Non-Model Organisms

4. Isolation of Apoplastic Fluid From Woody Plants Leaves: Grapevine and Coffee as a Case Study

Andreia Figueiredoand Leonor Guerra-Guimarães

5. Shotgun Proteomics for L3 and L4 Anisakis simplex Development Stages

6. A Primer and Guidelines for Shotgun Proteomic Analysis in Non-Model Organisms

Part III: Clinical Proteomics

7. SWATH-MS Protocols in Human Diseases

Maria del Pilar Chantada-Vázquez, María García Vence, Antonio Serna, Cristina Núñez Cand Susana B.Bravo

Lucía Lourido, Rocío Paz, Cristina Ruiz-Romero, Peter Nilsson and Francisco J. Blanco

9. Human Blood Plasma Investigation Employing
2d Uplc-Udms^e Data-Independent Acquisition Proteomics

Licia C. Silva-Costa, Bradley J. Smith, Pamela T. Carlson, Gustavo H. M. F. Souza, and Daniel Martins-de-Souza

Sjoerd van der Post and Liisa Arike

John Iradukunda, Tariq Ganief, Jonathan M. Blackburn and Nelson C. Soares

12. Proteogenomic Approach for Mycobacterium Tuberculosis Investigation

Part IV: Food Proteomics

Ana G. Abril, Ignacio Ortea, Jorge Barros-Velázquez, Tomás G. Villa, and Pilar Calo-Mata

14. Shotgun Proteomics and Protein-Based Bioinformatics for the Characterization of Food-Derived Bioactive Peptides

Mónica Carrera, Manuel Pazos, Santiago P. Aubourg and José M. Gallardo

Part V: Analysis of Postranslational Modifications and Protein Complexes

15. FTSC-labeling Coupled with 2DE-LC-MS/MS Analysis of Complex Protein Mixtures for Identification and Relative Quantification of Tissue Carbonylome

Lucía Méndez, Lorena Barros, Silvia Muñoz and Isabel Medina

16. Mass Spectrometry-Based Proteomics for Analysis of Hydrophilic Phosphopeptides

Chia-Feng Tsai, Jeffrey S. Smith, Dylan S. Eiger, Kendall Martin, Tao Liu, Richard D Smith, Tujin Shi, Sudarshan Rajagopal and Jon M. Jacobs

17. Rapid Shotgun Phosphoproteomics Analysis

Mónica Carrera, Benito Cañas and Daniel Lopez-Ferrer

18. System-wide Profiling Of Protein-Complexes Via Size Exclusion Chromatography–Mass Spectrometry (SEC-MS)

Fossati Andrea, Fabian Frommelt, Federico Uliana, Claudia Martelli, Matej Vizovisek, Ludovic Gillet, Collins Ben, Matthias Gstaiger andRuedi Aebersold

Part VI: Shotgun Proteomics Data Processing and Storage

19. Qualitative and Quantitative Shotgun Proteomics Data Analysis from Data-Dependent Acquisition Mass Spectrometry

Jesse G. Meyer

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts