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.

Table of Contents:
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 Transcriptomics 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.