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Plant Proteomics

Methods and Protocols

  • Book
  • © 2014

Overview

Editors:
  1. Jesus V. Jorrin-Novo

    1. Dept of Biochem & Molecular Bio, University of Cordoba, Cordoba, Spain

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  2. Setsuko Komatsu

    1. University of Tsukuba National Institute of Crop Science, Tsukuba, Japan

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  3. Wolfram Weckwerth

    1. Molecular Systems Biology, University of Vienna, Vienna, Austria

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  4. Stefanie Wienkoop

    1. Dept. Molecular Systems Biology, University of Vienna, Vienna, Austria

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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

Part of the book series: Methods in Molecular Biology (MIMB, volume 1072)

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Table of contents (53 protocols)

  1. Front Matter

    Pages i-xxi
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  2. Introductory

    1. Front Matter

      Pages 1-1
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    2. Plant Proteomics Methods and Protocols

      • Jesus V. Jorrin-Novo
      Pages 3-13

    3. From Proteomics to Systems Biology: MAPA, MASS WESTERN, PROMEX, and COVAIN as a User-Oriented Platform

      • Wolfram Weckwerth, Stefanie Wienkoop, Wolfgang Hoehenwarter, Volker Egelhofer, Xiaoliang Sun
      Pages 15-27

    4. Plant Proteomics: From Genome Sequencing to Proteome Databases and Repositories

      • Katsumi Sakata, Setsuko Komatsu
      Pages 29-42

    5. How to Use 2D Gel Electrophoresis in Plant Proteomics

      • Thierry Rabilloud
      Pages 43-50

    6. Standardization of Data Processing and Statistical Analysis in Comparative Plant Proteomics Experiment

      • Luis Valledor, M. Cristina Romero-Rodríguez, Jesus V. Jorrin-Novo
      Pages 51-60

    7. The Expanding Universe of Mass Analyzer Configurations for Biological Analysis

      • Juan J. Calvete
      Pages 61-81

  3. Experimental

    1. Front Matter

      Pages 83-83
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    2. 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-García, Antonio Jesús Castro
      Pages 85-91

    3. Making a Protein Extract from Plant Pathogenic Fungi for Gel- and LC-Based Proteomics

      • Raquel González Fernández, Inmaculada Redondo, Jesus V. Jorrin-Novo
      Pages 93-109

    4. Plant Proteomics Methods to Reach Low-Abundance Proteins

      • Egisto Boschetti, Pier Giorgio Righetti
      Pages 111-129

    5. Combination of 2DE and LC for Plant Proteomics Analysis

      • Sami Irar, Faiçal Brini, Khaled Masmoudi, Montserrat Pagès
      Pages 131-140

    6. 2DE Analysis of Forest Tree Proteins Using Fluorescent Labels and Multiplexing

      • Jenny Renaut, Céline Leclercq, Sébastien Planchon
      Pages 141-154

    7. Differential Plant Proteome Analysis by Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)

      • María J. Martínez-Esteso, Juan Casado-Vela, Susana Sellés-Marchart, María A. Pedreño, Roque Bru-Martínez
      Pages 155-169

    8. Global Quantitative Proteomics Using Spectral Counting: An Inexpensive Experimental and Bioinformatics Workflow for Deep Proteome Coverage

      • Tiago S. Balbuena, Diogo Ribeiro Demartini, Jay J. Thelen
      Pages 171-183

    9. Combining Chymotrypsin/Trypsin Digestion to Identify Hydrophobic Proteins from Oil Bodies

      • Martina Vermachova, Zita Purkrtova, Jiri Santrucek, Pascale Jolivet, Thierry Chardot, Milan Kodicek
      Pages 185-198

    10. Mass Western for Absolute Quantification of Target Proteins and Considerations About the Instrument of Choice

      • David Lyon, Wolfram Weckwerth, Stefanie Wienkoop
      Pages 199-208

    11. Selected Reaction Monitoring Mass Spectrometry: A Methodology Overview

      • H. Alexander Ebhardt
      Pages 209-222

    12. Mass Spectrometry-Based Imaging of Metabolites and Proteins

      • Manuela Peukert, Michael Becker, Andrea Matros, Hans-Peter Mock
      Pages 223-240
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Keywords

About this book

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.

Editors and Affiliations

  • Dept of Biochem & Molecular Bio, University of Cordoba, Cordoba, Spain

    Jesus V. Jorrin-Novo

  • University of Tsukuba National Institute of Crop Science, Tsukuba, Japan

    Setsuko Komatsu

  • Molecular Systems Biology, University of Vienna, Vienna, Austria

    Wolfram Weckwerth

  • Dept. Molecular Systems Biology, University of Vienna, Vienna, Austria

    Stefanie Wienkoop

Bibliographic Information

  • Book Title: Plant Proteomics

  • Book Subtitle: Methods and Protocols

  • Editors: Jesus V. Jorrin-Novo, Setsuko Komatsu, Wolfram Weckwerth, Stefanie Wienkoop

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-631-3

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2014

  • Hardcover ISBN: 978-1-62703-630-6Published: 18 October 2013

  • Softcover ISBN: 978-1-4939-6029-3Published: 17 September 2016

  • eBook ISBN: 978-1-62703-631-3Published: 17 October 2013

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XXI, 786

  • Number of Illustrations: 54 b/w illustrations, 75 illustrations in colour

  • Topics: Plant Sciences, Proteomics

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