Next Generation Proteomics for Clinical Biomarker Detection using SWATH-MS -- A Combined Chemical Derivatization/Mass Spectrometric Method for the Enhanced Detection and Relative Quantification of Protein Ubiquitination -- Assessment of Ubiquitin Chain Topology by Targeted Mass Spectrometry -- Quantitative Phosphoproteomic using Titanium Dioxide Micro-Columns and Label Free Quantitation -- Isotopic Labeling and Quantitative Proteomics of Acetylation on Histones and Beyond -- Quantitative Analysis of Protein S-Acylation Site Dynamics Using Site-Specific Acyl-Biotin Exchange (ssABE) -- Reducing Complexity? Cysteine Reduction and S-alkylation in Proteomic Workflows: Practical Considerations -- Detection of Unknown Chemical Adduct Modifications on Proteins: From Wet to Dry Laboratory -- Considerations for Identifying Endogenous Protein Complexes from Tissue via Immunoaffinity Purification and Quantitative Mass Spectrometry -- Metaproteomics of Freshwater Microbial Communities -- Peptide-to-Protein Summarization: An Important Step for Accurate Quantification In Label-Based Proteomics -- Experimental Design in Quantitative Proteomics -- Practical Integration of Multi-Run iTRAQ Data -- Quantitative Proteomics Data in the Public Domain: Challenges and Opportunities -- Computational Proteomics with Jupyter and Python -- The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis.

New insights into modern medicine and systems biology are enabled by innovative protocols and advanced technologies in mass spectrometry-based proteomics. This volume details new pipelines, workflows, and ways to process data that allow for new frontiers in proteomics to be pushed forward. With applications to biomarker discovery, interactions between proteins, between biological systems, dynamics of post-translational modifications among others, new protocols have been developed and iteratively refined to probe the endless complexity of the proteome in ever greater details. This volume deals with methods for data dependent and data independent mass spectrometry analyses. Valuable, first-hand information is provided from designing experiments, sample preparation and analysis, exploitation of public datasets and carrying out reproducible data pipelines, using modern computational tools such as Galaxy or Jupyter. 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, Mass Spectrometry of Proteins: Methods and Protocols aims to ensure successful results in the further study of this vital field. .