Plant Proteomics

Details:

Erscheinungsdatum:	30.09.2013
Medium:	Buch
Einband:	Gebunden
Titel:	Plant Proteomics
Titelzusatz:	Methods and Protocols
Auflage:	2. Auflage von 2014 2nd edition
Redaktion:	Jorrin-Novo, Jesus V. Komatsu, Setsuko Weckwerth, Wolfram Wienkoop, Stefanie
Verlag:	Springer-Verlag GmbH Humana Press
Sprache:	Englisch
Schlagworte:	Botanik SCIENCE Life Sciences Botany
Rubrik:	Botanik
Seiten:	786
Abbildungen:	128 illus., 70 illus. in color
Reihe:	Methods in Molecular Biology (Nr. 1072) Humana Press
Gewicht:	1640 gr
ISBN-13:	9781627036306
ISBN-10:	162703630X
Herstellernummer:	80084345
Zustand:	Neuware

Beschreibung:

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.

Inhaltsverzeichnis:

<p>Part I. Introductory</p><p> </p><p>1. Plant Proteomics Methods and Protocols </p><p> Jesús V. Jorrín Novo </p><p> </p><p>2. From Proteomics to Systems Biology: MAPA, MASS WESTERN, PROMEX and COVAIN as a User-Oriented Platform</p><p>Wolfram Weckerth, Stefanie Wienkoop, Volker Egelhofer, and Xiaoliang Sun</p><p> </p><p>3. Plant Proteomics: From Genome Sequencing to Proteome Databases and Repositories</p><p> Katsumi Sakata and Setsuko Komatsu</p><p> </p><p>4. How to Use 2D Gel Electrophoresis in Plant Proteomics</p><p> Thierry Rabilloud</p><p> </p><p>5. Standarization of Data Processing and Statistical Analysis in a 2-DE-Based Comparative Plant Proteomics Experiment </p><p> Luis Valledor, Cristina Romero, and Jesús V. Jorrín Novo</p><p> </p><p>6. The Expanding Universe of Mass Analyzer Configurations for Biological Analysis</p><p> Juan J. Calvete</p><p> </p><p> </p><p>Part II. Experimental</p><p> </p><p>7. A Protocol for Protein Extraction from Lipid-Rich Plant Tissues Suitable for Electrophoresis </p><p> Agnieszka Zienkiewicz, Juan David Rejón, Juan de Dios Alché, María Isabel Rodríguez, and Antonio Jesús Castro</p><p> </p><p>8. Making a Protein Extract in Plant Pathogenic Fungi for Gel- and LC-Based Proteomics</p><p> Raquel Gonzalez Fernandez, Inmaculada Redondo, and Jesus V. Jorrin Novo.</p><p> </p><p>9. Plant Proteomics Methods to Reach Low-Abundance Proteins </p><p>Egisto Boschetti and Pier Giorgio Righetti </p><p> </p><p>10. Combination of 2DE and LC for Plant Proteomics Analysis</p><p> Sami Irar, Faiçal Brini, Khaled Masmoudi, and Montserrat Pagès</p><p> </p><p>11. 2DE Analysis of Forest Tree Proteins Using Fluorescent Labels and Multiplexing</p><p> Jenny Renaut, Céline Leclercq, and Sébastien Planchon</p><p> </p><p>12. Differential Plant Proteome Analysis by Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)</p><p> María J. Martínez-Esteso, Juan Casado-Vela, Susana Sellés-Marchart, Mari A. Pedreño, and Roque Bru-Martínez</p><p> </p><p>13. Global Quantitative Proteomics Using Spectral Counting: An Inexpensive Experimental and Bioinformatics Workflow for Deep Proteome Coverage</p><p> Tiago S. Balbuena, Diogo Ribeiro Demartini, and Jay J. Thelen </p><p> </p><p>14. Combining Chymotrypsin/trypsin Digestion to Identify Hydrophobic Proteins from Oil Bodies</p><p> Martina Vermachova, Zita Purkrtova, Jiri Santrucek, Pascale Jolivet, Thierry Chardot, and Milan Kodicek</p><p> </p><p>15. Mass Western for Absolute Quantification of Target Proteins and Considerations About the Instrument of Choice</p><p> David Lyon, Wolfram Weckwerth, and Stefanie Wienkoop</p><p> </p><p>16. Selected Reaction Monitoring Mass Spectrometry: A Methodology Overview</p><p> Alexander Ebhardt</p><p> </p><p>17. Mass Spectrometry Based Imaging of Metabolites and Proteins</p><p> Manuela Peukert, Michael Becker, Andrea Matros, and Hans-Peter Mock</p><p> </p><p>18. Using the Yeast Two-Hybrid System to Identify Protein-Protein Interactions</p><p> Eduardo Rodríguez-Negrete, Eduardo R. Bejarano, and Araceli G. Castillo</p><p> </p><p>19. Modifications of Wheat Germ Cell-Free System for Functional Proteomics of Plant Membrane Proteins</p><p> Akira Nozawa and Yuzuru Tozawa</p><p> </p><p> </p><p>Part III. Biological Systems</p><p> </p><p>20. Arabidopsis Proteomics: A Simple and Standardizable Workflow for Quantitative Proteome Characterization</p><p> Anja Rödiger, Birgit Agne, Katja Baerenfaller, and Sacha Baginsky</p><p> </p><p>21. Analysis of Rice Proteins Using SDS-PAGE Shotgun Proteomics</p><p> Karlie A. Neilson, Iniga S. George, Samantha J. Emery, Sridevi Muralidharan, and Paul A. Haynes</p><p> </p><p>22. Medicago truncatula Proteomics for Systems Biology: Novel Rapid Shotgun LC-MS Approach for Relative Quantification Based on Full-Scan Selective Peptide Extraxtion (Selpex)</p><p> M. Angeles Castillejo, Christiana Staudinger, Volker Egelhofer, and Stefanie Wienkoop</p><p> </p><p>23. Soybean Proteomics</p><p> Zahed Hossain and Setsuko Komatsu</p><p> </p><p>24. Proteome Analysis of Orphan Plant Species, Fact or Fiction?</p><p> Sebastien Christian Carpentier, and Twan America</p><p> </p><p>25. An Improved Detergent-Compatible Gel-Fractionation LC-LTQ-Orbitrap-MS Workflow for Plant and Microbial Proteomics </p><p> Luis Valledor and Wolfram Weckwerth</p><p> </p><p> </p><p>Part IV. Descriptive Proteomics</p><p> </p><p>26. Seed Proteomics</p><p> Ján A. Miernyk </p><p> </p><p>27. Back to Osborne. Sequential Protein Extraction and LC-MS for Characterization of the Seed Proteome</p><p> María Cristina Romero Rodríguez, Ana M. Maldonado Alconada, and Jesús V. Jorrín-Novo</p><p> </p><p>28. Xylem Sap Proteomics</p><p> Thomas Duge de Bernonville, Cécile Albenne, Matthieu Arlat, Laurent Hoffmann, Emmanuelle lauber, and Elisabeth Jamet</p><p> </p><p>29. Suspension Cultured-Plant Cells as a Tool to Analyze the Extracellular Proteome</p><p> Ana B. Sabater-Jara, Lorena Almagro, Sarai Belchí-Navarro, Maria J. Martínez-Esteso, Sabri M. Youssef, Juan Casado-Vela, Juan C. Vera-Urbina, Susana Selles, Roque Bru, and Mari Angeles Pedreño</p><p> </p><p>30. Pollen Cultivation and Preparation for Proteome Studies</p><p> Heidi Pertl-Obermeyer and Gerhard Obermeyer</p><p> </p><p> </p><p>Part V. Subcellular Proteomics</p><p> </p><p>31. Isolation of the Plant Cytosolic Fraction for Proteomic Analysis</p><p> Gonzalo M. Estavillo, Yves Verhertbruggen, Barry J. Pogson, Joshua L. Heazlewood, Henrik V. Scheller, and Jun Ito</p><p> </p><p>32. Quantitative Proteomic Analysis of Intact Plastids</p><p> Takeshi Shiraya, Kentaro Kaneko, and Toshiaki Mitsui</p><p> </p><p>33. Shotgun Proteomics of Plant Plasma Membrane and Microdomain Proteins Using Nano-LC-MS/MS</p><p> Daisuke Takahashi, Bin Li, Takato Nakayama, Yukio Kawamura, and Matsuo Uemura</p><p> </p><p>34. Plant Mitochondrial Proteomics</p><p> Shaobai Huang, Richard P. Jacoby, A. Harvey Millar, and Nicolas L. Taylor</p><p> </p><p>35. Separation of the Plant Golgi Apparatus and Endoplasmic Reticulum by Free-Flow Electrophoresis</p><p> Harriet T. Parsons, Susana M. González Fernández-Niño, and Joshua L. Heazlewood</p><p> </p><p>36. Isolation of Leaf Peroxisomes from Arabidopsis for Organelle Proteomics Analyses</p><p> Sigrun Reumann and Rajneesh Singhal</p><p> </p><p> </p><p>Part VI. Comparative Proteomics</p><p> </p><p>37. Proteomics of Field Samples, the Case of the Chernobyl Area</p><p> Katarína Klubicová, Namik M. Rashydov, and Martin Hajduch</p><p> </p><p>38. Differential Proteome and Secretome Analysis During Rice-Pathogen Interaction</p><p> Yiming Wang, Sang Gon Kim, Jingni Wu, Sun Tae Kim, and Kyu Young Kang</p><p> </p><p>39. Protein Extraction and Gel-Based Separation Methods to Analyse Responses to Pathogens in Carnation (Dianthus caryophyllus L)</p><p> Harold Ardila, Raquel González Fernández, Blanca Ligia Higuera, Inmaculada Redondo, and Sixta Tulia Martínez</p><p> </p><p>
Part VII. Post-Translational Proteomics</p><p> </p><p>40. StageTip-Based HAMMOC, an Efficient and Inexpensive Phosphopeptide Enrichment Method for Plant Shotgun Phosphoproteomics </p><p> Hrofumi Nagakami </p><p> </p><p>41. Simultaneous Identification and Quantification of Nitrosylation Sites by Combination of Biotin Switch and ICAT Labeling</p><p>Abasse Fares, Claude Nespoulous, Michel Rossignol, and Jean-Benoît Peltier</p><p> </p><p>42. Tandem Metal-Oxide Affinity Chromatography for Enhanced Depth of Phosphoproteome Analysis</p><p> Gerold J.M. Beckers, Wolfgang Hoehenwarter, Horst Röhrig, Uwe Conrath, and Wolfram Weckwerth</p><p> </p><p>43. N-Glycoprotein Enrichment by Lectin Affinity Chromatography</p><p> Eliel Ruiz-May, Carmen Catalá, and Jocelyn K. C. Rose</p><p> </p><p>44. Rapid and High-Throughput N-glycomic Analysis of Plant Glycoproteins</p><p> Kentaro Kaneko, Takeshi Shiraya, Toshiaki Mitsui, and Shin-ichiro Nishimura</p><p> </p><p>45. Assay for Proteasome-Dependent Protein Degradation and Ubiquitinated Proteins</p><p> Takeo Sato, Kaori Sako, and Junji Yamaguchi</p><p> </p><p> </p><p>Part VIII. Interactomics and Proteinomics</p><p> </p><p>46. Separation of Membrane Protein Complexes by Native LDS-PAGE</p><p> Janine Arnold, Alexey Shapiguzov, Geoffrey Fucile, Jean-David Rochaix, Michel Goldschmidt-Clermont, Lutz Andreas Eichacker</p><p> </p><p>47. Identification of Thioredoxin Target Disulfides Using Isotope-Coded Affinity Tags</p><p> Per Hägglund, Jakob Bunkenborg, Kenji Maeda, Christine Finnie, and Birte Svensson</p><p> </p><p>48. Class III Peroxidases </p><p> Sabine Lüthje, Claudia-Nicole Meisrimler, David Hopff, Tim Schütze and Katrin Heino</p><p> </p><p> </p><p>IX. Translational Proteomics</p><p> </p><p>49. Proteotyping of Holm oak (Quercus ilex subsp. ballota) Provenances Through Proteomic Analysis of Acorn Flour</p><p> José Valero Galván, Raquel Gonzalez Fernandez, Luis Valledor, rafael Mª Navarro Cerrillo, and Jesús V. Jorrín Novo</p><p> </p><p>50. Immunoproteomics Analysis of Food Allergens</p><p> Rika Nakamura and Reiko Teshima</p><p> </p><p>51. Beer and Wort Proteomics</p><p> Takashi Iimure, Makoto Kihara, and Kazuhiro Sato</p><p> </p><p>52. Precipitation of Champagne Base Wine Proteins Prior 2D Electrophoresis</p><p> Clara Cilindre and Philippe Jeandet</p><p> </p><p>53. The Minimal Information About a Proteomics Experiment (MIAPE) from the Proteomics Standards Initiative</p><p> Salvador Martínez-Bartolomé, Pierre A. Binz, and Juan P. Albar</p>

Information:

Includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains key notes and implementation advice from the experts