Part I. Introductory

1. Plant Proteomics Methods and Protocols

Jes's V. Jorr n Novo

2. From Proteomics to Systems Biology: MAPA, MASS WESTERN, PROMEX and COVAIN as a User-Oriented Platform

Wolfram 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 Jes's V. Jorr n 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 Rej n, Juan de Dios Alch , Mar a Isabel Rodr guez, and Antonio Jes's 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, Fai al Brini, Khaled Masmoudi, and Montserrat Pag s

11. 2DE Analysis of Forest Tree Proteins Using Fluorescent Labels and Multiplexing

Jenny Renaut, C line Leclercq, and S bastien Planchon

12. Differential Plant Proteome Analysis by Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)

Mar a J. Mart nez-Esteso, Juan Casado-Vela, Susana Sell s-Marchart, Mari A. Pedre o, and Roque Bru-Mart nez

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 Rodr guez-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 R diger, 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 Biolog.