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.

Includes cutting-edge methods and protocols

Plant Proteomics Methods and Protocols.- From Proteomics to Systems Biology: MAPA, MASS WESTERN, PROMEX and COVAIN as a User-Oriented Platform.- Plant Proteomics: From Genome Sequencing to Proteome Databases and Repositories.- How to Use 2D Gel Electrophoresis in Plant Proteomics.- Standarization of Data Processing and Statistical Analysis in a 2-DE-Based Comparative Plant Proteomics Experiment.- The Expanding Universe of Mass Analyzer Configurations for Biological Analysis.- A Protocol for Protein Extraction from Lipid-Rich Plant Tissues Suitable for Electrophoresis.- Making a Protein Extract in Plant Pathogenic Fungi for Gel- and LC-Based Proteomics.- Plant Proteomics Methods to Reach Low-Abundance Proteins.- Combination of 2DE and LC for Plant Proteomics Analysis.- 2DE Analysis of Forest Tree Proteins Using Fluorescent Labels and Multiplexing.- Differential Plant Proteome Analysis by Isobaric Tags for Relative and Absolute Quantitation (iTRAQ).- Global Quantitative Proteomics Using Spectral Counting: An Inexpensive Experimental and Bioinformatics Workflow for Deep Proteome Coverage.- Combining Chymotrypsin/trypsin Digestion to Identify Hydrophobic Proteins from Oil Bodies.- Mass Western for Absolute Quantification of Target Proteins and Considerations About the Instrument of Choice.- Selected Reaction Monitoring Mass Spectrometry: A Methodology Overview.- Mass Spectrometry Based Imaging of Metabolites and Proteins.- Using the Yeast Two-Hybrid System to Identify Protein-Protein Interactions.- Modifications of Wheat Germ Cell-Free System for Functional Proteomics of Plant Membrane Proteins.- Arabidopsis Proteomics: A Simple and Standardizable Workflow for Quantitative Proteome Characterization.- Analysis of Rice Proteins Using SDS-PAGE Shotgun Proteomics.- Medicago truncatula Proteomics for Systems Biology: Novel Rapid Shotgun LC-MS Approach for Relative Quantification Based on Full-Scan Selective Peptide Extraxtion (Selpex).- Soybean Proteomics.- Proteome Analysis of Orphan Plant Species, Fact or Fiction?.- An Improved Detergent-Compatible Gel-Fractionation LC-LTQ-Orbitrap-MS Workflow for Plant and Microbial Proteomics.- Seed Proteomics.- Back to Osborne. Sequential Protein Extraction and LC-MS for Characterization of the Seed Proteome.- Xylem Sap Proteomics.- Suspension Cultured-Plant Cells as a Tool to Analyze the Extracellular Proteome.- Pollen Cultivation and Preparation for Proteome Studies.- Isolation of the Plant Cytosolic Fraction for Proteomic Analysis.- Quantitative Proteomic Analysis of Intact Plastids.- Shotgun Proteomics of Plant Plasma Membrane and Microdomain Proteins Using Nano-LC-MS/MS.- Plant Mitochondrial Proteomics.- Separation of the Plant Golgi Apparatus and Endoplasmic Reticulum by Free-Flow Electrophoresis.- Isolation of Leaf Peroxisomes from Arabidopsis for Organelle Proteomics Analyses.- Proteomics of Field Samples, the Case of the Chernobyl Area.- Differential Proteome and Secretome Analysis During Rice-Pathogen Interaction.- Protein Extraction and Gel-Based Separation Methods to Analyse Responses to Pathogens in Carnation (Dianthus caryophyllus L).- StageTip-Based HAMMOC, an Efficient and Inexpensive Phosphopeptide Enrichment Method for Plant Shotgun Phosphoproteomics.- Simultaneous Identification and Quantification of Nitrosylation Sites by Combination of Biotin Switch and ICAT Labeling.- Tandem Metal-Oxide Affinity Chromatography for Enhanced Depth of Phosphoproteome Analysis.- N-Glycoprotein Enrichment by Lectin Affinity Chromatography.- Rapid and High-Throughput N-glycomic Analysis of Plant Glycoproteins.- Assay for Proteasome-Dependent Protein Degradation and Ubiquitinated Proteins.- Separation of Membrane Protein Complexes by Native LDS-PAGE.- Identification of Thioredoxin Target Disulfides Using Isotope-Coded Affinity Tags.- Class III Peroxidases.- Proteotyping of Holm oak (Quercus ilex subsp. ballota) Provenances Through Proteomic Analysis of Acorn Flour.- Immunoproteomics Analysis of Food Allergens.- Beer and Wort Proteomics.- Precipitation of Champagne Base Wine Proteins Prior 2D Electrophoresis.- The Minimal Information About a Proteomics Experiment (MIAPE) from the Proteomics Standards Initiative.