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Life Sciences - Plant Sciences | Plant Proteomics - Methods and Protocols

Plant Proteomics

Methods and Protocols

Series: Methods in Molecular Biology, Vol. 1072

Jorrin-Novo, J.V., Komatsu, S., Weckwerth, W., Wienkoop, S. (Eds.)

2nd ed. 2014, XXI, 786 p. 129 illus., 75 illus. in color.

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

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.

Content Level » Professional/practitioner

Keywords » bioinformatics - electrophoresis - interactomics - plant biology - proteomics - systems biology

Related subjects » Biochemistry & Biophysics - Plant Sciences

Table of contents 

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

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