Mass Spectrometry-driven Proteomics: An Introduction -- Metabolic Labeling of Model Organisms using Heavy Nitrogen (15N) -- Trypsin-catalyzed Oxygen-18 Labeling for Quantitative Proteomics -- ICPL Labeling Strategies for Proteome Research -- Quantitative Proteome Analysis using Isobaric Peptide Termini Labeling (IPTL) -- Complete Chemical Modification of Amine and Acid Functional Groups of Peptides and Small Proteins -- Production and Use of Stable-isotope-labeled Proteins for Absolute Quantitative Proteomics -- Organelle Proteomics -- Membrane Protein Digestion - Comparison of LPI Hexalane with Traditional Techniques -- GeLCMS for In-depth Protein Characterization and Advanced Analysis of Proteomes -- Exploring New Proteome Space: Combining Lys-N Proteolytic Digestion and Strong Cation Exchange (SCX) Separation in Peptide Centric MS-driven Proteomics -- Quantitation of Newly Synthesized Proteins by Pulse-labeling with Azidohomoalanine -- Analytical Strategies in Mass Spectrometry Based Phosphoproteomics -- A Protocol on the Use of Titanium Dioxide Chromatography for Phosphoproteomics -- Positional Proteomis at the N-terminus as a Means of Proteome Simplification -- N-terminomics: A High-content Screen for Protease Substrates and their Cleavage Sites -- Protease Specificity Profiling by Tandem Mass Spectrometry Using Proteome-derived Peptide Libraries -- Identification of Proteolytic Products and Natural Protein N-termini by Terminal Amine Isotopic Labeling of Substrates (TAILS) -- Lectins as Tools to Select for Glycosylated Proteins -- Strong Cation Exchange Chromatography for Analysis of Sialylated Glycopeptides -- Titanium Dioxide Enrichment of Sialic Acid-containing Glycopeptides -- Chemical de-O-Glycosylation of Glycoproteins for Applications in LC-based Proteomics -- Ubiquitination and Degradation of Proteins -- Bioinformatics Challenges in Mass Spectrometry Driven Proteomics -- A Case Study on the Comparison of Different Software Tools for Automated Quantification of Peptides.

Proteomics by means of mass spectrometry has rapidly changed the way that we analyze proteomes. Gel-Free Proteomics: Methods and Protocols addresses contemporary methods for gel-free proteome research with a special focus on differential analysis and protein modifications. Divided into twenty-five chapters, this detailed volume meticulously describes vital procedures needed to perform gel-free proteomics, ranging from sample preparation, isotope labeling for differential proteomics, enrichment technologies for modified proteins and peptides, and bioinformatics. 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, Gel-Free Proteomics: Methods and Protocols serves as a timely resource for both professionals and novices pursuing research in this critical field.