Table of Contents

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.