Part I: Multiprotein Complexes and Protein-Protein Interactions

1. One- and Two-Dimensional Blue Native (BN) PAGE and Immunodetection of Low-Abundance Chloroplast Membrane Protein Complexes

Shingo Kikuchi, Jocelyn Bédard, and Masato Nakai

2. Analysis of Thylakoid Protein Complexes by Two Dimensional Electrophoretic Systems

Sari Sirpiö, Marjaana Suorsa, and Eva-Mari Aro

3. Preparation of Multiprotein Complexes from Arabidopsis Chloroplasts Using Tandem Affinity Purification

Charles Andrès, Birgit Agne, and Felix Kessler

4. Studying Interactions between Chloroplast Proteins in Intact Plant Cells Using Bimolecular Fluorescence Complementation (BiFC) and Förster Resonance Energy Transfer (FRET)

Jodi Maple and Simon G. Møller

5. Studying Chloroplast Protein Interactions In Vitro: An Overview of the Available Methods

Joanna Tripp and Enrico Schleiff

Part II: Omics and Large-Scale Analyses

6. Proteome Databases and Other Online Resources for Chloroplast Research in Arabidopsis

Diogo Ribeiro Demartini, Célia Regina Carlini, and Jay J. Thelen

7. Use of Transcriptomics to Analyse Chloroplast Processes in Arabidopsis

Tatjana Kleine and Dario Leister

8. Use of Non-Aqueous Fractionation and Metabolomics to Study Chloroplast Function in Arabidopsis

Peter Geigenberger, Axel Tiessen, and Jörg Meurer

9. Chloroplast Phenomics: Systematic Phenotypic Screening of Chloroplast Protein Mutants in Arabidopsis

Yan Lu, Linda J. Savage, and Robert L. Last

Part III: Proteomics and Suborganellar Fractionation

10. Preparation of Envelope Membrane Fractions from Arabidopsis Chloroplasts for Proteomic Analysis and Other Studies

Daniel Salvi, Lucas Moyet, Daphné Seigneurin-Berny, Myriam Ferro, Jacques Joyard, and Norbert Rolland

11. Preparation of Stroma, Thylakoid Membrane, and Lumen Fractions from Arabidopsis thaliana Chloroplasts for Proteomic Analysis

Michael Hall, Yogesh Mishra, and Wolfgang P. Schröder

12. Preparation of Plastoglobules from Arabidopsis Plastids for Proteomic Analysis and Other Studies

Celine Besagni, Lucia Eugeni Piller, and Claire Bréhélin

13. Preparation and Proteomic Analysis of Chloroplast Ribosomes

Kenichi Yamaguchi

14. The Workflow for Quantitative Proteome Analysis of Chloroplast Development and Differentiation, Chloroplast Mutants, and Protein Interactions by Spectral Counting

Giulia Friso, Paul Dominic B. Olinares, and Klaas J. van Wijk

15. Use of Phosphoproteomics to Study Post-Translational Protein Modifications in Arabidopsis Chloroplasts

Anne Endler and Sacha Baginsky

Part IV: Photosynthesis and Biochemical Analysis

16. Use of a Pulse-Amplitude Modulated (PAM) Chlorophyll Fluorometer to Study the Efficiency of Photosynthesis in Arabidopsis Plants

Matthew D. Brooks and Krishna K. Niyogi

17. Gas Exchange Measurements for the Determination of Photosynthetic Efficiency in Arabidopsis Leaves

Giles Johnson and Erik Murchie

18. Measurement of the ΔpH and Electric Field Developed Across Arabidopsis Thylakoids in the Light