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
