Plant proteomics : methods and protocols
著者
書誌事項
Plant proteomics : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 2139）（Springer protocols）
Humana Press, c2020
3rd ed
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注記
Other editors: Luis Valledor, Mari Angeles Castillejo, Maria-Dolores Rey
Previous ed.: 2014
Includes bibliographical references and indexes
収録内容
- What is new in (plant) proteomics methods and protocols: the 2015-2019 quinquennium / Jesus V. Jorrin-Novo
- Multiple biomolecule isolation protocol compatible with mass spectrometry and other high-throughput analyses in microalgae / Francisco Colina, María Carbó, Ana Alvarez, Mónica Meijón, María Jesús Cañal, and Luis Valledor
- Protein interaction networks: functional and statistical approaches / Mónica Escandón, Laura Lamelas, Víctor Roces, Víctor M. Guerrero-Sanchez, Mónica Meijón, and Luis Valledor
- Specific protein database creation from transcriptomics data in nonmodel species: holm oak (Quercus ilex L.) / Víctor M. Guerrero-Sanchez, Ana M. Maldonado-Alconada, Rosa Sánchez-Lucas, and Maria-Dolores Rey
- Subcellular proteomics in conifers: purification of nuclei and chloroplast proteomes / Laura Lamelas, Lara García, María Jesús Cañal, and Mónica Meijón
- Apoplastic fluid preparation from Arabidopsis thaliana leaves upon interaction with a nonadapted powdery mildew pathogen / Ryohei Thomas Nakano, Nobuaki Ishihama, Yiming Wang, Junpei Takagi, Tomohiro Uemura, Paul Schulze-Lefert, and Hirofumi Nakagami
- 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
- A protocol for the plasma membrane proteome analysis of rice leaves / Ravi Gupta, Yu-Jin Kim, and Sun Tae Kim
- Isolation, purity assessment, and proteomic analysis of endoplasmic reticulum / Xin Wang and Setsuko Komatsu
- 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
- Quantitative profiling of protein abundance and phosphorylation state in plant tissues using tandem mass tags / Gaoyuan Song, Christian Montes, and Justin W. Walley
- 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 Mari Angeles Castillejo
- Combining targeted and untargeted data acquisition to enhance quantitative plant proteomics experiments / Gene Hart-Smith
- A phosphoproteomic analysis pipeline for peels of tropical fruits / Janet Juarez-Escobar, José M. Elizalde-Contreras, Víctor M. Loyola-Vargas, and Eliel Ruiz-May
- Label-free quantitative phosphoproteomics for algae / Megan M. Ford, Sheldon R. Lawrence II, Emily G. Werth, Evan W. McConnell, and Leslie M. Hicks
- Targeted quantification of phosphopeptides by parallel reaction monitoring (PRM) / Sara Christina Stolze and Hirofumi Nakagami
- Enrichment of N-linked glycopeptides and their identification by complementary fragmentation techniques / Eduardo Antonio Ramirez-Rodriguez and Joshua L. Heazlewood
- High-resolution lysine acetylome profiling by offline fractionation and immunoprecipitation / Jonas Giese, Ines Lassowskat, and Iris Finkemeier
- 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
- In vivo cross-linking to analyze transient protein-protein interactions / Heidi Pertl-Obermeyer and Gerhard Obermeyer
- Proteome analysis of 14-3-3 targets in tomato fruit tissues / Yongming Luo, Yu Lu, Junji Yamaguchi, and Takeo Sato
- The use of proteomics in search of allele-specific proteins in (allo) polyploid crops / Sebastien Christian Carpentier
- Methods for optimization of protein extraction and proteogenomic mapping in sweet potato / Thualfeqar Al-Mohanna, Norbert T. Bokros, Nagib Ahsan, George V. Popescu, and Sorina C. Popescu
- In silico analysis of class III peroxidases: hypothetical structure, ligand binding sites, posttranslational modifications, and interaction with substrates / Sabine Lüthje and Kalaivani Ramanathan
- MALDI mass spectrometry imaging of peptides in Medicago truncatula root nodules / Caitlin Keller, Erin Gemperline, and Lingjun Li
- Cystatin activity-based protease profiling to select protease inhibitors useful in plant protection / Marie-Claire Goulet, Frank Sainsbury, and Dominique Michaud
- A pipeline for the metabolic pathway reconstruction in plant orphan species / Cristina López-Hidalgo, Mónica Escandón, Luis Valledor, and Jesus V. Jorrin-Novo
- Detection of plant low-abundance proteins by means of combinatorial peptide ligand library methods / Egisto Boschetti and Pier Giorgio Righetti
- iTRAQ-based proteomic analysis of rice grains / Marouane Baslam, Kentaro Kaneko, and Toshiaki Mitsui
内容説明・目次
内容説明
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.
目次
- 1. What is New in (Plant) Proteomics Methods and Protocols: the 2015-2019 Quinquennium Jesus V. Jorrin-Novo 2. Multiple Biomolecule Isolation Protocol Compatible with Mass Spectrometry and Other High Throughput Analyses in Microalgae Francisco Colina, Maria Carbo, Ana Alvarez, Monica Meijon, Maria Jesus Canal, and Luis Valledor 3. Protein Interaction Networks: Functional and Statistical Approaches Monica Escandon, Laura Lamelas, Victor F. Roces, Victor M. Guerrero-Sanchez, Monica Meijon, and Luis Valledor 4. Specific Protein Database Creation From Transcriptomics Data In Non-Model Species: Holm oak (Quercus ilex L.) Victor M. Guerrero-Sanchez, Ana M. Maldonado-Alconada, Rosa Sanchez-Lucas, and Maria-Dolores Rey 5. Subcellular Proteomics in Conifers: Purification of Nuclei and Chloroplast Proteomes Laura Lamelas, Lara Garcia, Maria Jesus Canal, and Monica Meijon 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-Sanchez, Jaime A. Morante-Carriel, Ascension Martinez-Marquez, Susana Selles-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 Gomez-Galvez, Rosa Sanchez-Lucas, Bonoso San-Eufrasio, Luis Enrique Rodriguez de Francisco, Ana M. Maldonado-Alconada, Carlos Fuentes-Almagro, and M. Angeles 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, Jose M. Elizalde-Contreras, Victor 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 Nee, 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 Luthje 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 Lopez-Hidalgo, Monica Escandon, Luis Valledor, and Jesus V. Jorrin-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
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