Plant Proteomics: Methods and Protocols

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