Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts

Introduction to Mass Spectrometry-based Proteomics.- LC-MS Spectra Processing.- Isotopic Distributions.- Retention Time Prediction and Protein Identification.- Comparing Peptide Spectra Matches Across Search Engines.- Calculation of False Discovery Rate for Peptide and Protein Identification.- Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry.- Interpretation of Tandem Mass Spectra of Posttranslationally Modified Peptides.- Solution to Dark Matter Identified by Mass-tolerant Database Search.- Phosphoproteomics Profiling to Identify Altered Signaling Pathways and Kinase-targeted Cancer Therapies.- Mass Spectrometry Based Characterization of Ub- and UbL-modified Proteins.- Targeted Proteomics as a Tool for Quantifying Urine-based Biomarkers.- Data Imputation in Merged Isobaric Labelling-based Relative Quantification Datasets.- Clustering Clinical Data in R.- Review of Issues and Solutions to Data Analysis Reproducibility and Data Qualityin Clinical Proteomics.- Review of Batch Effects Prevention, Diagnostics, and Correction Approaches.- Using the Object-oriented PowerShell for Simple Proteomics Data Analysis.- Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data.