Analysis of Organelles by On-Line Two-Dimensional Liquid Chromatography-Tandem Mass Spectrometry -- Analysis of Organelles by On-Line Two-Dimensional Liquid Chromatography-Tandem Mass Spectrometry -- Analysis of Organelles, Vesicles, and Protein Machineries -- Purification and Proteomic Analysis of Chloroplasts and their Sub-Organellar Compartments -- Proteomic Analysis of the Stacked Golgi Complex -- Purification of Saccharomyces cerevisiae Mitochondria by Zone Electrophoresis in a Free Flow Device -- Preparation of Respiratory Chain Complexes from Saccharomyces cerevisiae Wild-Type and Mutant Mitochondria -- Mitochondrial Proteomics -- Purification and Proteomic Analysis of the Mouse Liver Mitochondrial Inner Membrane -- Subcellular Fractionation and Proteomics of Nuclear Envelopes -- Purification and Proteomic Analysis of a Nuclear-Insoluble Protein Fraction -- Preparation Methods of Human Metaphase Chromosomes for their Proteome Analysis -- Purification and Proteomic Analysis of Plant Plasma Membranes -- Protocol to Enrich and Analyze Plasma Membrane Proteins from Frozen Tissues -- Proteomic Characterization of Membrane Protein Topology -- Free Flow Isoelectric Focusing -- Use of Gas-Phase Fractionation to Increase Protein Identifications -- Purification and Proteomic Analysis of Lysosomal Integral Membrane Proteins -- Affinity Purification of Soluble Lysosomal Proteins for Mass Spectrometric Identification -- Purification and Proteomic Analysis of Synaptic Vesicles -- Purification and Proteomics Analysis of Pancreatic Zymogen Granule Membranes -- Isolation and Proteomic Analysis of Chlamydomonas Centrioles -- Purification and Proteomic Analysis of 20S Proteasomes from Human Cells -- Characterization of E. coli Ribosomal Particles -- Cellular, Genetic and Molecular Mechanisms of Plant Embryogenesis -- Assessment of Organelle Purity Using Antibodies and Specific Assays -- Identifying Bona Fide Components of an Organelle by Isotope-Coded Labeling of Subcellular Fractions -- Determination of Genuine Residents of Plant Endomembrane Organelles using Isotope Tagging and Multivariate Statistics -- Quantitative Proteomic Analysis to Profile Dynamic Changes in the Spatial Distribution of Cellular Proteins -- Use of Transcriptomic Data to Support Organelle Proteomic Analysis.

Proteomic analyses have proven to be an invaluable tool in obtaining high-throughput protein identification from low-abundance, complex biological samples. In Organelle Proteomics, detailed protocols provide step-by-step instructions to successfully study organelle proteomes by performing the purification of the various organelles present in eukaryotic cells, as well as by preparing certain sub-fractions of organelles. A series of chapters cover the whole analytical procedure of organelle characterization, from its purification starting with whole cells up to protein identification using mass spectrometry. Devoted to methods enabling a global estimate of the reliability of the protein list assigned to an organelle, Organelle Proteomics allows scientists to gain a vital and important understanding of organelle study.