Table of Contents

Twelve Years of Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC).- Stable Isotope Labeling by Amino Acids Applied to Bacterial Cell Culture.- SILAC Labeling of Yeast for the Study of Membrane Protein Complexes.- Whole Proteome Analysis of the Protozoan Parasite Trypanosoma brucei using Stable Isotope Labeling by Amino Acids in Cell Culture and Mass Spectrometry.- Stable Isotope Labeling by Amino Acids in Cultured Primary Neurons.- SILAC and Alternatives in Studying Cellular Proteomes of Plants.- In Vivo Stable Isotope Labeling by Amino Acids in Drosophila melanogaster.- Stable Isotope Labeling for Proteomic Analysis of Tissues in Mouse.- Identification of Novel Protein Functions and Signaling Mechanisms by Genetics and Quantitative Phosphoproteomics in Caenorhabditis elegans.- SILAC-based Temporal Phosphoproteomics.- Global Ubiquitination Analysis by SILAC in Mammalian Cells.- Quantifying In Vivo, Site-specific Changes in Protein Methylation with SILAC.- Applying SILAC for the Differential Analysis of Protein Complexes.- Defining Dynamic Protein Interactions Using SILAC-based Quantitative Mass Spectrometry.- Identifying Nuclear Protein-Protein Interactions using GFP Affinity Purification and SILAC-based Quantitative Mass Spectrometry.- Analyzing the Protein Assembly and Dynamics of the Human Spliceosome with SILAC.- Identification and Validation of Protein-Protein Interactions by Combining Co-immunoprecipitation, Antigen Competition, and Stable Isotope Labeling.- Protein Correlation Profiling-SILAC to Study Protein-Protein Interactions.- Autophagosomal Proteome Analysis by Protein Correlation Profiling-SILAC.- Design and Application of Super-SILAC for Proteome Quantification.- Proteomics Meets Genetics: SILAC Labeling of Drosophila melanogaster Larvae and Cells for In Vivo Functional Studies.- Analysis of Secreted Proteins using SILAC.- Identification of MicroRNA Targets by Pulsed SILAC.- MaxQuant forIn-Depth Analysis of Large SILAC Datasets.