Description
Book SynopsisThis 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 biolog
Table of Contents
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. Barrachina and Ángel García
3. Utilization of Laser Capture Microdissection Coupled to Mass Spectrometry to Uncover the Proteome of Cellular Protrusions
Ana Gordon and 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 Figueiredo and Leonor Guerra-Guimarães
5. Shotgun Proteomics for L3 and L4 Anisakis simplex Development Stages
Robert Stryiński, Jesús Mateos, Elżbieta Łopieńska-Biernat, and Mónica Carrera
6. A Primer and Guidelines for Shotgun Proteomic Analysis in Non-Model Organisms
Angel P. Diz
and Paula Sánchez-Marín
Part III: Clinical Proteomics
7. SWATH-MS Protocols in Human Diseases
Maria del Pilar Chantada-Vázquez, María García Vence, Antonio Serna, Cristina Núñez C and Susana B. Bravo
8. Serum Proteomic Profiling in Rheumatoid Arthritis by Antibody Suspension Bead Arrays
Lucía Lourido, Rocío Paz, Cristina Ruiz-Romero, Peter Nilsson and Francisco J. Blanco
9. Human Blood Plasma Investigation Employing
2d Uplc-Udmse Data-Independent Acquisition Proteomics
Licia C. Silva-Costa, Bradley J. Smith, Pamela T. Carlson, Gustavo H. M. F. Souza, and Daniel Martins-de-Souza
10. Metaproteomics Analysis of Host-Microbiota Interfaces
Sjoerd van der Post and Liisa Arike
11. Mass Spectrometry-Based Analysis of Mycobacterial Single-Colony Proteome
John Iradukunda, Tariq Ganief, Jonathan M. Blackburn and Nelson C. Soares
12. Proteogenomic Approach for Mycobacterium Tuberculosis Investigation
Julia Bespyatykh, Georgij Arapidi, and Egor Shitikov
Part IV: Food Proteomics
13. Shotgun Proteomics for Food Microorganism Detection
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 and Ruedi 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
20. The jPOST Repository as a Public Data Repository for Shotgun Proteomics
Yu Watanabe, Akiyasu C. Yoshizawa, Yasushi Ishihama and Shujiro Okuda
