Introduction to Mass Spectrometry-Based Proteomics -- LC-MS Spectra Processing -- Isotopic Distributions -- Retention Time Prediction and Protein Identification -- Algorithms for Database Dependent Search of MSMS Data -- Interpretation of Tandem Mass Spectra of Post-Translationally Modified Peptides -- Improving Peptide Identification Using Empirical Scoring Systems -- Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry -- Computational Approaches to Selected Reaction Monitoring (SRM) Assay Design -- Feature Selection and Machine Learning with Mass Spectrometry Data -- Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data -- Permethylated N-Glycan Analysis with Mass Spectrometry -- Mass Spectrometry Methods for Studying Glycosylation in Cancer -- Proteomics Data Exchange and Storage: The Need for Common Standards and Public Repositories -- Tools for Protein Post Translational Modifications Analysis: FAK, A Case Study -- Proteomic Strategies to Characterize Signaling Pathways -- Simple Proteomics Data Analysis in the Object-Oriented PowerShell.

Since the publishing of the first edition, the methodologies and instrumentation involved in the field of mass spectrometry-based proteomics has improved considerably.  Fully revised and expanded, Mass Spectrometry Data Analysis in Proteomics, Second Edition presents expert chapters on specific MS-based methods or data analysis strategies in proteomics. The volume covers data analysis topics relevant for quantitative proteomics, post translational modification, HX-MS, glycomics, and data exchange standards, among other topics.  Written in the highly successful Methods in Molecular Biology series format, chapters include brief introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.   Updated and authoritative, Mass Spectrometry Data Analysis in Proteomics, Second Edition serves as a detailed guide for all researchers seeking to further our knowledge in the field of proteomics.