ISBN-13: 9781493960293 / Angielski / Miękka / 2016 / 786 str.
ISBN-13: 9781493960293 / Angielski / Miękka / 2016 / 786 str.
This book presents recent advances made in the field of proteomics and their application to plant biology and translational research. It features step-by-step, readily reproducible protocols as well as notes on troubleshooting and avoiding known pitfalls.
Part I. Introductory
1. Plant Proteomics Methods and Protocols
Jesús V. Jorrín 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 Jesús V. Jorrín 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 Rejón, Juan de Dios Alché, María Isabel Rodríguez, and Antonio Jesús 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, Faiçal Brini, Khaled Masmoudi, and Montserrat Pagès
11. 2DE Analysis of Forest Tree Proteins Using Fluorescent Labels and Multiplexing
Jenny Renaut, Céline Leclercq, and Sébastien Planchon
12. Differential Plant Proteome Analysis by Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)
María J. Martínez-Esteso, Juan Casado-Vela, Susana Sellés-Marchart, Mari A. Pedreño, and Roque Bru-Martínez
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 Rodríguez-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 Rödiger, 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 Biology: Novel Rapid Shotgun LC-MS Approach for Relative Quantification Based on Full-Scan Selective Peptide Extraxtion (Selpex)
M. Angeles Castillejo, Christiana Staudinger, Volker Egelhofer, and Stefanie Wienkoop
23. Soybean Proteomics
Zahed Hossain and Setsuko Komatsu
24. Proteome Analysis of Orphan Plant Species, Fact or Fiction?
Sebastien Christian Carpentier, and Twan America
25. An Improved Detergent-Compatible Gel-Fractionation LC-LTQ-Orbitrap-MS Workflow for Plant and Microbial Proteomics
Luis Valledor and Wolfram Weckwerth
Part IV. Descriptive Proteomics
26. Seed Proteomics
Ján A. Miernyk
27. Back to Osborne. Sequential Protein Extraction and LC-MS for Characterization of the Seed Proteome
María Cristina Romero Rodríguez, Ana M. Maldonado Alconada, and Jesús V. Jorrín-Novo
28. Xylem Sap Proteomics
Thomas Duge de Bernonville, Cécile Albenne, Matthieu Arlat, Laurent Hoffmann, Emmanuelle lauber, and Elisabeth Jamet
29. Suspension Cultured-Plant Cells as a Tool to Analyze the Extracellular Proteome
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
30. Pollen Cultivation and Preparation for Proteome Studies
Heidi Pertl-Obermeyer and Gerhard Obermeyer
Part V. Subcellular Proteomics
31. Isolation of the Plant Cytosolic Fraction for Proteomic Analysis
Gonzalo M. Estavillo, Yves Verhertbruggen, Barry J. Pogson, Joshua L. Heazlewood, Henrik V. Scheller, and Jun Ito
32. Quantitative Proteomic Analysis of Intact Plastids
Takeshi Shiraya, Kentaro Kaneko, and Toshiaki Mitsui
33. Shotgun Proteomics of Plant Plasma Membrane and Microdomain Proteins Using Nano-LC-MS/MS
Daisuke Takahashi, Bin Li, Takato Nakayama, Yukio Kawamura, and Matsuo Uemura
34. Plant Mitochondrial Proteomics
Shaobai Huang, Richard P. Jacoby, A. Harvey Millar, and Nicolas L. Taylor
35. Separation of the Plant Golgi Apparatus and Endoplasmic Reticulum by Free-Flow Electrophoresis
Harriet T. Parsons, Susana M. González Fernández-Niño, and Joshua L. Heazlewood
36. Isolation of Leaf Peroxisomes from Arabidopsis for Organelle Proteomics Analyses
Sigrun Reumann and Rajneesh Singhal
Part VI. Comparative Proteomics
37. Proteomics of Field Samples, the Case of the Chernobyl Area
Katarína Klubicová, Namik M. Rashydov, and Martin Hajduch
38. Differential Proteome and Secretome Analysis During Rice-Pathogen Interaction
Yiming Wang, Sang Gon Kim, Jingni Wu, Sun Tae Kim, and Kyu Young Kang
39. Protein Extraction and Gel-Based Separation Methods to Analyse Responses to Pathogens in Carnation (Dianthus caryophyllus L)
Harold Ardila, Raquel González Fernández, Blanca Ligia Higuera, Inmaculada Redondo, and Sixta Tulia Martínez
Part VII. Post-Translational Proteomics
40. StageTip-Based HAMMOC, an Efficient and Inexpensive Phosphopeptide Enrichment Method for Plant Shotgun Phosphoproteomics
Hrofumi Nagakami
41. Simultaneous Identification and Quantification of Nitrosylation Sites by Combination of Biotin Switch and ICAT Labeling
Abasse Fares, Claude Nespoulous, Michel Rossignol, and Jean-Benoît Peltier
42. Tandem Metal-Oxide Affinity Chromatography for Enhanced Depth of Phosphoproteome Analysis
Gerold J.M. Beckers, Wolfgang Hoehenwarter, Horst Röhrig, Uwe Conrath, and Wolfram Weckwerth
43. N-Glycoprotein Enrichment by Lectin Affinity Chromatography
Eliel Ruiz-May, Carmen Catalá, and Jocelyn K. C. Rose
44. Rapid and High-Throughput N-glycomic Analysis of Plant Glycoproteins
Kentaro Kaneko, Takeshi Shiraya, Toshiaki Mitsui, and Shin-ichiro Nishimura
45. Assay for Proteasome-Dependent Protein Degradation and Ubiquitinated Proteins
Takeo Sato, Kaori Sako, and Junji Yamaguchi
Part VIII. Interactomics and Proteinomics
46. Separation of Membrane Protein Complexes by Native LDS-PAGE
Janine Arnold, Alexey Shapiguzov, Geoffrey Fucile, Jean-David Rochaix, Michel Goldschmidt-Clermont, Lutz Andreas Eichacker
47. Identification of Thioredoxin Target Disulfides Using Isotope-Coded Affinity Tags
Per Hägglund, Jakob Bunkenborg, Kenji Maeda, Christine Finnie, and Birte Svensson
48. Class III Peroxidases
Sabine Lüthje, Claudia-Nicole Meisrimler, David Hopff, Tim Schütze and Katrin Heino
IX. Translational Proteomics
49. Proteotyping of Holm oak (Quercus ilex subsp. ballota) Provenances Through Proteomic Analysis of Acorn Flour
José Valero Galván, Raquel Gonzalez Fernandez, Luis Valledor, rafael Mª Navarro Cerrillo, and Jesús V. Jorrín Novo
50. Immunoproteomics Analysis of Food Allergens
Rika Nakamura and Reiko Teshima
51. Beer and Wort Proteomics
Takashi Iimure, Makoto Kihara, and Kazuhiro Sato
52. Precipitation of Champagne Base Wine Proteins Prior 2D Electrophoresis
Clara Cilindre and Philippe Jeandet
53. The Minimal Information About a Proteomics Experiment (MIAPE) from the Proteomics Standards Initiative
Salvador Martínez-Bartolomé, Pierre A. Binz, and Juan P. Albar
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.
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