Multiplexed Quantitative Proteomics for High-Throughput Comprehensive Proteome Comparisons of Human Cell Lines.- ample Preparation Approaches for iTRAQ Labelling and Quantitative Proteomic Analyses in Systems Biology.- Two birds with One Stone: Parallel Quantification of Proteome and Phospho-Proteome Using iTRAQ -- Selected Reaction Monitoring to Measure Proteins of Interest in Complex Samples: A Practical Guide.- Monitoring PPARG Induced Changes in Glycolysis by Selected Reaction Monitoring Mass Spectrometry.- A Targeted MRM Approach for Tempo-Spatial Proteomics Analyses.- Targeted Phospho-Proteome Analysis Using Selected/Multiple Reaction Monitoring (SRM/MRM) -- Testing Suitability of Cell Cultures for SILAC-Experiments Using SWATH-Mass Spectrometry.- Combining Amine-Reactive Cross-Linkers and Photo-Reactive Amino Acids for 3D-Structure Analysis of Proteins and Protein Complexes.- Tissue MALDI Mass Spectrometry Imaging (MALDI MSI) of Peptides -- Ethyl Esterification for MALDI-MS Analysis of Protein Glycosylation.- Characterization of Protein N-Glycosylation by Analysis of ZIC-HILIC-Enriched Intact Proteolytic Glycopeptides.- Simple and Effective Affinity Purification Procedures for Mass Spectrometry-Based Identification of Protein-Protein Interactions in Cell Signaling Pathways.- A Systems Approach to Understand Antigen Presentation and the Immune Response -- Profiling of Smal l Molecules by Chemical Proteomics.- Generating Sample Specific Databases for Mass Spectrometry Based Proteomic Analysis by Using RNA Sequencing.- A Proteomic Workflow Using High Throughput De Novo Sequencing towards Complementation of Genome Information for Improved Comparative Crop Science -- From Phospho-Proteome to Modelling of Plant Signalling Pathways.- Interpretation of Quantitative Shotgun Proteomic Data.- A Simple Workflow for Large Scale Shotgun Glycoproteomics.- Systemic Analysis of Regulated Functional Networks.  .

This volume presents an overview of contemporary quantitative proteomics methods along with instructions on data interpretation, while providing examples on how to implement proteomics into systems biology. 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. Thorough and practical, Proteomics in Systems Biology: Methods and Protocols is a valuable resource for researchers who are interested in using proteomics techniques to help answer biological and medical questions.