Plant Proteomics (3^rd Ed., 3rd ed. 2020) Methods and Protocols Methods in Molecular Biology Series, Vol. 2139

This third edition detailsrecent advances made in the field of proteomics and the application to plant biology and translational research. In recent years, improvements have been made to protocols on high-throughput proteomics at all workflow stages, from wet to dry labs. Chapters are divided into nine parts, covering methods and protocols such as applications of gel-free, label- or label-free, imaging and targeted approaches to experimental model systems, crops and orphan species, study and analysis of PTMs, protein interactions, specific families of proteins, and finally proteomics in translational research. 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, Plant Proteomics: Methods and Protocols, Third Edition aims to ensure successful results in the further study of this vital field.

1. What is New in (Plant) Proteomics Methods and Protocols: the 2015-2019 Quinquennium

Jesús V. Jorrín-Novo

2. Multiple Biomolecule Isolation Protocol Compatible with Mass Spectrometry and Other High Throughput Analyses in Microalgae

Francisco Colina, María Carbó, Ana Álvarez, Mónica Meijón, María Jesús Cañal, and Luis Valledor

3. Protein Interaction Networks: Functional and Statistical Approaches

Mónica Escandón, Laura Lamelas, Víctor F. Roces, Víctor M. Guerrero-Sanchez, Mónica Meijón, and Luis Valledor

4. Specific Protein Database Creation From Transcriptomics Data In Non-Model Species: Holm oak (Quercus ilex L.)

Victor M. Guerrero-Sanchez, Ana M. Maldonado-Alconada, Rosa Sánchez-Lucas, and María-Dolores Rey

Laura Lamelas,Lara García, María Jesús Cañal, and Mónica Meijón

6. Apoplastic fluid preparation from Arabidopsis thaliana leaves upon interaction with a Non-Adapted Powdery Mildew Pathogen

Ryohei Thomas Nakano, Nobuaki Ishihama, Yiming Wang, Junpei Takagi, Tomohiro Uemura, Paul Schulze-Lefert, and Hirofumi Nakagami

7. Shotgun Proteomics of Plant Plasma Membrane and Microdomain Proteins Using Nano-LC-MS/MS

Daisuke Takahashi, Bin Li, Takato Nakayama, Yukio Kawamura, and Matsuo Uemura

8. A Protocol for the Plasma Membrane Proteome Analysis of Rice Leaves

Ravi Gupta, Yu-Jin Kim, and Sun Tae Kim

9. Isolation, Purity Assessment, and Proteomic Analysis of Endoplasmic Reticulum

Xin Wangand Setsuko Komatsu

10. Dimethyl Labeling-based Quantitative Proteomics of Recalcitrant Cocoa Pod Tissue

Yoel Esteve-Sánchez, Jaime A. Morante-Carriel, Ascensión Martínez-Márquez, Susana Sellés-Marchart, and Roque Bru-Martinez

11. Quantitative Profiling of Protein Abundance and Phosphorylation State in Plant Tissues using Tandem Mass Tags

Gaoyuan Song, Christian Montes, and Justin W Walley

12. Optimizing Shotgun Proteomics Analysis for a Confident Protein Identification and Quantitation in Orphan Plant Species; the case of Holm oak (Quercus ilex)

Isabel Gómez-Gálvez, Rosa Sánchez-Lucas, Bonoso San-Eufrasio, Luis Enrique Rodríguez de Francisco, Ana M. Maldonado-Alconada, Carlos Fuentes-Almagro, and M. Ángeles Castillejo

13. Combining Targeted and Untargeted Data Acquisition To Enhance Quantitative Plant Proteomics Experiments

Gene Hart-Smith

15. Label-Free Quantitative Phosphoproteomics for Algae

Megan M. Ford, Sheldon R. Lawrence II, Emily G. Werth, Evan W. McConnell, and Leslie M. Hicks

16. Targeted Quantification of Phosphopeptides by Parallel Reaction Monitoring (PRM)

Sara Christina Stolze and Hirofumi Nakagami

17. Enrichment of N-linked Glycopeptides and their Identification by Complementary Fragmentation Techniques

Eduardo Antonio Ramirez-Rodriguez, and Joshua L. Heazlewood

Jonas Giese, Ines Lassowskat, and Iris Finkemeier

20. In vivo cross-linking to Analyse Transient Protein-Protein Interactions

Heidi Pertl-Obermeyer and Gerhard Obermeyer

21. Proteomic Analysis of 14-3-3 Targets in Tomato Fruit Tissues

Yongming Luo, Yu Lu, Junji Yamaguchi, and Takeo Sato

Sebastien Christian Carpentier

23. Methods for Optimization of Protein Extraction and Proteogenomic Mapping in Sweetpotato

Thualfeqar Al-Mohanna, Norbert T. Bokros, Nagib Ahsan , George V. Popescu, and Sorina C. Popescu

24. In silico Analysis of Class III peroxidases: Hypothetical Structure, Ligand Binding-Sites, Post-Translational Modifications and Interaction with Substrates

Sabine Lüthje and Kalaivani Ramanathan

25. MALDI Mass Spectrometry Imaging of Peptides in Medicago truncatula Root Nodules

Caitlin Keller, Erin Gemperline, and Lingjun Li

26. Cystatin Activity-Based Protease Profiling to Select Protease Inhibitors Useful in Plant Protection

Marie-Claire Goulet, Frank Sainsbury, and Dominique Michaud

27. Pipeline for the Metabolic Pathway Reconstruction in Plant Orphan Species

Cristina López-Hidalgo, Mónica Escandón, Luis Valledor, and Jesús V. Jorrín-Novo

Egisto Boschetti and Pier Giorgio Righetti

29. iTRAQ-based Proteomic Analysis of Rice Grains

Marouane Baslam, Kentaro Kaneko, and Toshiaki Mitsui

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts