Plant Proteomics: Methods and Protocols, Second Edition presents recent advances made in the field of proteomics and their application to plant biology and translational research. In recent years, improvements in techniques and protocols for high-throughput proteomics have been made at all workflow stages, from wet (sampling, tissue and cell fractionation, protein extraction, depletion, purification, separation, MS analysis, quantification) to dry lab (experimental design, algorithms for protein identification, bioinformatics tools for data analysis, databases, and repositories). Divided into nine convenient sections, chapters cover topics such as applications of gel-free, label- or label-free, imaging and targeted approaches to experimental model systems, crops and orphan species, as well as the study and analysis of PTMs, protein interactions, and specific families of proteins, and finally proteomics in translational research. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Plant Proteomics: Methods and Protocols, Second Edition seeks to serve both professionals and novices looking to exploit the full potential of proteomics in plant biology research.

InhaltsangabePart I. Introductory 1. Plant Proteomics Methods and Protocols                 Jesús V. Jorrín Novo  2. From Proteomics to Systems Biology: MAPA, MASS WESTERN, PROMEX and COVAIN as a User-Oriented PlatformWolfram Weckerth, Stefanie Wienkoop, Volker Egelhofer, and Xiaoliang Sun 3. Plant Proteomics: From Genome Sequencing to Proteome Databases and Repositories                Katsumi Sakata and Setsuko Komatsu 4. How to Use 2D Gel Electrophoresis in Plant Proteomics                Thierry Rabilloud 5. Standarization of Data Processing and Statistical Analysis in a 2-DE-Based Comparative Plant Proteomics Experiment                 Luis Valledor, Cristina Romero, and Jesús V. Jorrín Novo 6. The Expanding Universe of Mass Analyzer Configurations for Biological Analysis                Juan J. Calvete  Part II. Experimental 7. A Protocol for Protein Extraction from Lipid-Rich Plant Tissues Suitable for Electrophoresis                 Agnieszka Zienkiewicz, Juan David Rejón, Juan de Dios Alché, María Isabel Rodríguez, and Antonio Jesús Castro 8. Making a Protein Extract in Plant Pathogenic Fungi for Gel- and LC-Based Proteomics                Raquel Gonzalez Fernandez, Inmaculada Redondo, and Jesus V. Jorrin Novo. 9. Plant Proteomics Methods to Reach Low-Abundance Proteins Egisto Boschetti and Pier Giorgio Righetti  10. Combination of 2DE and LC for Plant Proteomics Analysis                Sami Irar, Faiçal Brini, Khaled Masmoudi, and Montserrat  Pagès 11. 2DE Analysis of Forest Tree Proteins Using Fluorescent Labels and Multiplexing                Jenny Renaut, Céline Leclercq, and Sébastien Planchon 12. Differential Plant Proteome Analysis by Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)                María J. Martínez-Esteso, Juan Casado-Vela, Susana Sellés-Marchart, Mari A. Pedreño, and Roque Bru-Martínez 13. Global Quantitative Proteomics Using Spectral Counting: An Inexpensive Experimental and Bioinformatics Workflow for Deep Proteome Coverage                Tiago S. Balbuena, Diogo Ribeiro Demartini, and Jay J. Thelen  14. Combining Chymotrypsin/trypsin Digestion to Identify Hydrophobic Proteins from Oil Bodies                Martina Vermachova, Zita Purkrtova, Jiri Santrucek, Pascale Jolivet, Thierry Chardot, and Milan Kodicek 15. Mass Western for Absolute Quantification of Target Proteins and Considerations About the Instrument of Choice                David Lyon, Wolfram Weckwerth, and Stefanie Wienkoop 16. Selected Reaction Monitoring Mass Spectrometry: A Methodology Overview                Alexander Ebhardt 17. Mass Spectrometry Based Imaging of Metabolites and Proteins                Manuela Peukert, Michael Becker, Andrea Matros, and Hans-Peter Mock 18. Using the Yeast Two-Hybrid System to Identify Protein-Protein Interactions                Eduardo Rodríguez-Negrete, Eduardo R. Bejarano, and Araceli G. Castillo 19. Modifications of Wheat Germ Cell-Free System for Functional Proteomics of Plant Membrane Proteins                Akira Nozawa and Yuzuru Tozawa  Part III. Biological Systems 20. Arabidopsis Proteomics: A Simple and Standardizable Workflow for Quantitative Proteome Characterization                Anja Rödiger, Birgit Agne, Katja Baerenfaller, and Sacha Baginsky 21. Analysis of Rice Proteins Using SDS-PAGE Shotgun Proteomics                Karlie A. Neilson, Iniga S. George, Samantha J. Emery, Sridevi Muralidharan, and Paul A. Haynes 22. Medicago truncatula Proteomics for Systems Biology: Novel Rapid Shotg