A Robust Protocol for Protein Extraction and Digestion -- Improving Proteome Coverage and Sample Recovery with Enhanced FASP (Efasp) For Quantitative Proteomic Experiments -- Proteome Characterization of a Chromatin Locus using the Proteomics of Isolated Chromatin Segments Approach -- Profiling Cell Lines Nuclear Sub-Proteome -- Optimized Enrichment of Phosphoproteomes by Fe-IMAC Column Chromatography -- Full Membrane Protein Coverage Digestion And Quantitative Bottom-Up Mass Spectrometry Proteomics -- Hydrophilic Strong Anion Exchange (Hsax) Chromatography Enables Deep Fractionation Of Tissue Proteomes -- High Ph Reversed-Phase Micro-Columns for Simple, Sensitive and Efficient Fractionation of Proteome and (TMT-Labeled) Phosphoproteome Digests -- Multi-Lectin Affinity Chromatography for Separation, Identification, and Quantitation of Intact Protein Glycoforms in Complex Biological Mixtures -- Parallel Exploration of Interaction Space by Bioid and Affinity Purification Coupled to Mass Spectrometry -- LUMIER: A Discovery Tool for Mammalian Protein Interaction Networks -- Dual Color, Multiplex Analysis of Protein Microarrays for Precision Medicine -- Quantitative Proteomics Using SILAC -- Relative Protein Quantification using Tandem Mass Tag Mass Spectrometry -- Pathway-Informed Discovery and Targeted Proteomic Workflows Using Mass Spectrometry -- Generation of High Quality SWATH Acquisition Data for Label-Free Quantitative Proteomics Studies Using Tripletof® Mass Spectrometers -- Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols -- Protein Micropatterning Assay - Quantitative Analysis of Protein-Protein Interactions -- Designing Successful Proteomics Experiments -- Automated SWATH Data Analysis using Targeted Extraction of Ion Chromatograms -- Virtualization of Legacy Instrumentation Control Computers for Improved Reliability, Operational Life, and Management -- Statistical Assessment of QC Metrics on Raw LC-MS/MS Data -- Data Conversion with proteoWizard msConvert.

This volume aims to provide protocols on a wide range of biochemical methods, analytical approaches, and bioinformatics tools developed to analyze the proteome. 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, Proteomics: Methods and Protocols aims to ensure successful results in the further study of this vital field.