This third edition details recent advances made in the field of proteomics and the application to plant biology and translational research. In recent years, improvements have been made to protocols on high-throughput proteomics at all workflow stages, from wet to dry labs. Chapters are divided into nine parts, covering methods and protocols such as applications of gel-free, label- or label-free, imaging and targeted approaches to experimental model systems, crops and orphan species, study and analysis of PTMs, protein interactions, specific families of proteins, and finally proteomics in translational research. Written in the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge,Plant Proteomics: Methods and Protocols, Third Edition aims to ensure successful results in the further study of this vital field.
What is New in (Plant) Proteomics Methods and Protocols: the 2015-2019 Quinquennium.- Multiple Biomolecule Isolation Protocol Compatible with Mass Spectrometry and Other High Throughput Analyses in Microalgae.- Protein Interaction Networks: Functional and Statistical Approaches.- Specific Protein Database Creation From Tranillegalscriptomics Data In Non-Model Species: Holm oak (Quercus ilex L.).- Subcellular Proteomics in Conifers: Purification of Nuclei and Chloroplast Proteomes.- Apoplastic fluid preparation from Arabidopsis thaliana leaves upon interaction with a Non-Adapted Powdery Mildew Pathogen.- Shotgun Proteomics of Plant Plasma Membrane and Microdomain Proteins Using Nano-LC-MS/MS.- A Protocol for the Plasma Membrane Proteome Analysis of Rice Leaves.- Isolation, Purity Assessment, and Proteomic Analysis of Endoplasmic Reticulum.- Dimethyl Labeling-based Quantitative Proteomics of Recalcitrant Cocoa Pod Tissue.- Quantitative Profiling of Protein Abundance and Phosphorylation State in Plant Tissues using Tandem Mass Tags.- Optimizing Shotgun Proteomics Analysis for a Confident Protein Identification and Quantitation in Orphan Plant Species; the case of Holm oak (Quercus ilex).- Combining Targeted and Untargeted Data Acquisition To Enhance Quantitative Plant Proteomics Experiments.- Phosphoproteomic Pipeline in Peels of Tropical Fruits.- Label-Free Quantitative Phosphoproteomics for Algae.- Targeted Quantification of Phosphopeptides by Parallel Reaction Monitoring (PRM).- Enrichment of N-linked Glycopeptides and their Identification by Complementary Fragmentation Techniques.- High Resolution Lysine Acetylome Profiling By Offline Fractionation and Immunoprecipitation.- A Versatile Workflow for the Identification of Protein-Protein Interactions using GFP-Trap Beads And Mass Spectrometry-Based Label-Free Quantification.- In vivo cross-linking to Analyse Transient Protein-Protein Interactions.- Proteomic Analysis of 14-3-3 Targets in Tomato Fruit Tissues.- The use of Proteomics in Search 0f Allele Specific Proteins in (allo)polyploid Crops.- Methods for Optimization of Protein Extraction and Proteogenomic Mapping in Sweetpotato.- In silico Analysis of Class III peroxidases: Hypothetical Structure, Ligand Binding-Sites, Post-Translational Modifications and Interaction with Substrates.- MALDI Mass Spectrometry Imaging of Peptides in Medicago truncatula Root Nodules.- Cystatin Activity-Based Protease Profiling to Select Protease Inhibitors Useful in Plant Protection.- Pipeline for the Metabolic Pathway Reconstruction in Plant Orphan Species.- Detection of Plant Low-Abundance Proteins By Means Of Combinatorial Peptide Ligand Library Methods.- iTRAQ-based Proteomic Analysis of Rice Grains.
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Inhaltsverzeichnis
1. What is New in (Plant) Proteomics Methods and Protocols: the 2015-2019 Quinquennium
Jesús V. Jorrín-Novo
2. Multiple Biomolecule Isolation Protocol Compatible with Mass Spectrometry and Other High Throughput Analyses in Microalgae
Francisco Colina, María Carbó, Ana Álvarez, Mónica Meijón, María Jesús Cañal, and Luis Valledor
3. Protein Interaction Networks: Functional and Statistical Approaches
Mónica Escandón, Laura Lamelas, Víctor F. Roces, Víctor M. Guerrero-Sanchez, Mónica Meijón, and Luis Valledor
4. Specific Protein Database Creation From Tranillegalscriptomics Data In Non-Model Species: Holm oak (Quercus ilex L.)
Victor M. Guerrero-Sanchez, Ana M. Maldonado-Alconada, Rosa Sánchez-Lucas, and María-Dolores Rey
5. Subcellular Proteomics in Conifers: Purification of Nuclei and Chloroplast Proteomes
Laura Lamelas, Lara García, María Jesús Cañal, and Mónica Meijón
6. Apoplastic fluid preparation from Arabidopsis thaliana leaves upon interaction with a Non-Adapted Powdery Mildew Pathogen
Ryohei Thomas Nakano, Nobuaki Ishihama, Yiming Wang, Junpei Takagi, Tomohiro Uemura, Paul Schulze-Lefert, and Hirofumi Nakagami
7. 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
8. A Protocol for the Plasma Membrane Proteome Analysis of Rice Leaves
Ravi Gupta, Yu-Jin Kim, and Sun Tae Kim
9. Isolation, Purity Assessment, and Proteomic Analysis of Endoplasmic Reticulum
Xin Wang and Setsuko Komatsu
10. Dimethyl Labeling-based Quantitative Proteomics of Recalcitrant Cocoa Pod Tissue
Yoel Esteve-Sánchez, Jaime A. Morante-Carriel, Ascensión Martínez-Márquez, Susana Sellés-Marchart, and Roque Bru-Martinez
11. Quantitative Profiling of Protein Abundance and Phosphorylation State in Plant Tissues using Tandem Mass Tags
Gaoyuan Song, Christian Montes, and Justin W Walley
12. Optimizing Shotgun Proteomics Analysis for a Confident Protein Identification and Quantitation in Orphan Plant Species; the case of Holm oak (Quercus ilex)
Isabel Gómez-Gálvez, Rosa Sánchez-Lucas, Bonoso San-Eufrasio, Luis Enrique Rodríguez de Francisco, Ana M. Maldonado-Alconada, Carlos Fuentes-Almagro, and M. Ángeles Castillejo
13. Combining Targeted and Untargeted Data Acquisition To Enhance Quantitative Plant Proteomics Experiments
Gene Hart-Smith
14. Phosphoproteomic Pipeline in Peels of Tropical Fruits Janet Juarez-Escobar, José M. Elizalde-Contreras, Víctor M. Loyola-Vargas and Eliel Ruiz-May
15. Label-Free Quantitative Phosphoproteomics for Algae
Megan M. Ford, Sheldon R. Lawrence II, Emily G. Werth, Evan W. McConnell, and Leslie M. Hicks
16. Targeted Quantification of Phosphopeptides by Parallel Reaction Monitoring (PRM)
Sara Christina Stolze and Hirofumi Nakagami
17. Enrichment of N-linked Glycopeptides and their Identification by Complementary Fragmentation Techniques
Eduardo Antonio Ramirez-Rodriguez, and Joshua L. Heazlewood
18. High Resolution Lysine Acetylome Profiling By Offline Fractionation and Immunoprecipitation
Jonas Giese, Ines Lassowskat, and Iris Finkemeier
19. A Versatile Workflow for the Identification of Protein-Protein Interactions using GFP-Trap Beads And Mass Spectrometry-Based Label-Free Quantification Guillaume Née, Priyadarshini Tilak, and Iris Finkemeier
20. In vivo cross-linking to Analyse Transient Protein-Protein Interactions
Heidi Pertl-Obermeyer and Gerhard Obermeyer
21. Proteomic Analysis of 14-3-3 Targets in Tomato Fruit Tissues
Yongming Luo, Yu Lu, Junji Yamaguchi, and Takeo Sato
22. The use of Proteomics in Search 0f Allele Specific Proteins in (allo)polyploid Crops
Sebastien Christian Carpentier
23. Methods for Optimization of Protein Extraction and Proteogenomic Mapping in Sweetpotato
Thualfeqar Al-Mohanna , Norbert T. Bokros , Nagib Ahsan , George V. Popescu, and Sorina C. Popescu
24. In silico Analysis of Class III peroxidases: Hypothetical Structure, Ligand Binding-Sites, Post-Translational Modifications and Interaction with Substrates
Sabine Lüthje and Kalaivani Ramanathan
25. MALDI Mass Spectrometry Imaging of Peptides in Medicago truncatula Root Nodules
Caitlin Keller, Erin Gemperline, and Lingjun Li
26. Cystatin Activity-Based Protease Profiling to Select Protease Inhibitors Useful in Plant Protection
Marie-Claire Goulet, Frank Sainsbury, and Dominique Michaud
27. Pipeline for the Metabolic Pathway Reconstruction in Plant Orphan Species
Cristina López-Hidalgo, Mónica Escandón, Luis Valledor, and Jesús V. Jorrín-Novo
28. Detection of Plant Low-Abundance Proteins By Means Of Combinatorial Peptide Ligand Library Methods
Egisto Boschetti and Pier Giorgio Righetti
29. iTRAQ-based Proteomic Analysis of Rice Grains
Marouane Baslam, Kentaro Kaneko, and Toshiaki Mitsui
Klappentext
This third edition details recent advances made in the field of proteomics and the application to plant biology and translational research. In recent years, improvements have been made to protocols on high-throughput proteomics at all workflow stages, from wet to dry labs. Chapters are divided into nine parts, covering methods and protocols such as applications of gel-free, label- or label-free, imaging and targeted approaches to experimental model systems, crops and orphan species, study and analysis of PTMs, protein interactions, specific families of proteins, and finally proteomics in translational research. Written in the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge,Plant Proteomics: Methods and Protocols, Third Edition aims to ensure successful results in the further study of this vital field.
Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
