Quantitative Methods in Proteomics

This second edition provides new and updated methods on the principles underlying modern protein analysis, from statistical issues to gel-based and mass spectrometry-based applications. Chapters detail protein quantification as basis for realisation of quantitative studies, gel-based and mass spectrometry-based quantification techniques, TMT, IPTL, PRM, MALDI Imaging, SILAC, PTM analysis, DIA, cross-linking, and the up-to-date topics of software and data analysis. 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,  Quantitative Methods in Proteomics, Second Edition aims to provide comprehensive and competent overview in the important and still growing field of quantitative proteomics.

Important Issues in Planning a Proteomics Experiment: Statistical Considerations of Quantitative Proteomic Data.- Good Old-Fashioned Protein Concentration Determination by Amino Acid Analysis.- Protein Quantification using the “Rapid Western Blot” Approach.- The Whereabouts of 2D Gels in Quantitative Proteomics.- Proteome Analysis with Classical 2D-PAGE.- Silver Staining of 2D Electrophoresis Gels.- Differential Proteome Analysis using 2D-DIGE.- Quantitative Mass Spectrometry-Based Proteomics: An Overview.- Tandem Mass Tags for Comparative and Discovery Proteomics.- An Approach for Triplex-IPTL.- Targeted Protein Quantification Using Parallel Reaction Monitoring (PRM).- Quantitative Approach using Matrix Assisted Laser Desorption/Ionization Time of Flight (MALDI-ToF) Mass Spectrometry.- Application of SILAC Labeling in Phosphoproteomics Analysis.- Relative Quantification Of Phosphorylated and Glycosylated Peptides from the Same Sample using Isobaric Chemical Labelling with a Two-step Enrichment Strategy.- High Throughput Profiling of Proteome and Posttranslational Modifications by 16-plex TMT Labeling and Mass Spectrometry.- Quantification and Identification of Post-Translational Modifications using Modern Proteomics Approaches.- Affinity-enrichment Chemoproteomics for Target Deconvolution and Selectivity Profiling.- 2nSILAC for Quantitative Proteomics of Prototrophic Baker's Yeast.- Metabolic Labeling of Clostridioides difficile Proteins.- Application of Label-Free Proteomics for Quantitative Analysis of Urothelial Carcinoma and Cystitis Tissue.- Quantitative MS Workflow for a High-Quality Secretome Analysis by a Quantitative Secretome-proteome Comparison.- Establishing a Custom-Fit Data Independent Acquisition Method for Label Free Proteomics.- Label-free Proteomics Of Quantity-Limited Samples Using Ion Mobility-Assisted Data-Independent Acquisition Mass Spectrometry.- DIA-MS^Eto Study Microglial Function in Schizophrenia.- Detailed Method for Performing the ExSTA Approach in Quantitative Bottom-up Plasma Proteomics.- Quantitative Cross-Linking of Proteins and Protein Complexes.- Missing Value Monitoring to Address Missing Values in Quantitative Proteomics.- Quantitative Proteome Data Analysis of Tandem Mass Tags Labeled Samples.- Mining Protein Expression Databases Using Network Meta-Analysis.- A Tutorial for Variance-sensitive Clustering And The Quantitative Analysis Of Protein Complexes.- Automated Workflow for Peptide-level Quantitation from DIA/ SWATH-MS Data.