Provides up-to-date methods and protocols for plant proteomics, each written by expert researchers from leading laboratories. Experimental methodologies are explained in clear and complete detail for both the wet and dry laboratories. The methods and protocols presented in this volume will inspire the novice as well as the expert researcher to undertake new experimental endeavors in plant proteomics. Chapters 1 and 2 describe standard protocols and chapters 3 through 10 contain optimized protocols for protein extraction of tissues such as cereal seeds, xylem, phloem sap, of woody plants, and of cellular compartments, such as chloroplasts and mitochondria. These methods rely on improvements to solubilization of proteins, which is the emphasis of Chapters 11 and 12. Chapters 13 to 23 outline methods for protein identification, including 2DLC or LC of intact proteins, mass spectrometry (MALDI-TOF and MS/MS) with proteins separated by 2D gels, blue native ID gels, and Edman sequencing. Chapters 24 to 29 focus on the rapidly expanding area of analysis of post-translational modifications and protein-protein relationships. Attention is also given to data that proteomics produces, including management of that data, and to statistical tools used for effective analysis.
Total Protein Extraction with TCA-Acetone Valerie Mechin, Catherine Damerval and Michel Zivy Phenol Extraction of Proteins for Proteomic Studies of Recalcitrant Plant Tissues Mireille Faurobert, Esther Pelpoir and Jamila Chaib Protein Extraction from Cereal Seeds Gerard Branlard and Emmanuelle Bancel Protein Extraction from Xylem and Phloem Sap Julia Kehr and Martijn Rep Protein Extraction from Woody Plants Christophe Plomion and Celine Lalanne Isolation of Chloroplast Proteins from Arabidopsis thaliana for Proteome Analysis Klaas J. van Wijk, Jean-Benoit Peltier and Lisa Giacomelli Isolation and Sub-Fractionation of Plant Mitochondria for Proteomic Analysis Holger Eubel, Joshua L. Heazlewood and A. Harvey Millar Extraction of Nuclear Proteins from Root Meristematic Cells Fernando Gonzalez-Camacho and Francisco Javier Medina Isolation of Nuclear Proteins Setsuko Komatsu Isolation of Cell Wall Proteins from Medicago sativa Stems Bonnie S. Watson and Lloyd W. Sumner Plant Plasma Membrane Protein Extraction and Solubilization for Proteomic Analysis Veronique Santoni Detergents and Chaotropes for Protein Solubilization before Two-Dimensional Electrophoresis Thierry Rabilloud, Sylvie Luche, Veronique Santoni and Mireille Chevallet Two-Dimensional Electrophoresis for Plant Proteomics Walter Weiss and Angelika Gorg Visible and Fluorescent Staining of Two-Dimensional Gels Francois Chevalier, Valerie Rofidal and Michel Rossignol Two-Dimensional Differential In-Gel Electrophoresis (DIGE) of Leaf and Roots of Lycopersicon esculentum Matthew Keeler, Jessica Letarte, Emily Hattrup, Fatimah Hickman and Paul A. Haynes Quantitative Analysis of 2D Gels Michel Zivy Multivariate Data Analysis of Proteome Data Kare Engkilde, Susanne Jacobsen and Ib Sondergaard Edman Sequencing of Plant Proteins from 2D Gels Setsuko Komatsu Peptide Mass Fingerprinting, Identification of Proteins by Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF) Nicolas Sommerer, Delphine Centeno and Michel Rossignol Protein Identification using Nano Liquid Chromatography: Tandem Mass Spectrometry Luc Negroni Two-Dimensional Nanoflow Liquid Chromatography: Tandem Mass Spectrometry of Proteins Extracted from Rice Leaves and Roots Linda Breci and Paul A. Haynes Separation, Identification and Profiling of Membrane Proteins by GFC/ IEC/SDS-PAGE and MALDI TOF MS Wojciech Szponarski, Frederic Delom, Nicolas Sommerer, Michel Rossignol and Remy Gibrat The PROTICdb Database for 2-DE Proteomics Olivier Langella, Michel Zivy and Johann Joets Identification of Phosphorylated Proteins Maria V. Turkina and Alexander V. Vener Plant Proteomics and Glycosylation Anne-Catherine Fitchette, Olivia Tran Dinh, Loic Faye and Muriel Bardor Blue-Native Gel Electrophoresis for the Characterization of Protein Complexes in Plants Jesco Heinemeyer, Dagmar Lewejohann and Hans-Peter Braun Electroelution of Intact Proteins from SDS-PAGE Gels and Their Subsequent MALDI-TOF MS Analysis Zhentian Lei, Ajith Anand, Kirankumar S. Mysore and Lloyd W. Sumner Generation of Plant Protein Microarrays and Investigation of Antigen-Antibody Interactions Birgit Kersten and Tanja Feilner Phosphorylation Studies Using Plant Protein Microarrays Tanja Feilner and Birgit Kersten
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