Subcellular proteomics

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Abstract
I. Introduction: The Need for a Repertoire of Proteome Analysis Strategies as the Analytical Complement 28 II. Rationale of Proteome Analysis at the Level of Subcellular Structures 29 III. Analytical Tools in Subcellular Proteomics 29 A. Protein‐Identification Strategies Successfully Used in Subcellular Proteomics 30 B. Subcellular Fractionation 31 C. Strategies to Validate Subcellular Proteomics Data 33 IV. Examples of Subcellular Proteome Mapping Studies 34 A. Functional Architecture of the Nucleus 34 1. Nuclear Envelope (NE) 34 2. Nuclear Pore Complex (NPC) 35 3. Interchromatin Granule Clusters 40 4. Nucleous 40 5. Other Subnuclear Structures 40 B. Proteomic Analysis of Small Organelles and Vesicles 41 1. Golgi Apparatus 41 2. Mitochondria 41 3. Chloroplasts 42 4. Peroxisomes 43 5. Other Organelles 44 C. Subcellular Proteomics at the Level of Tissue‐Specific Structures: the Synapse 44 V. Monitoring Dynamic Changes in the Subcellullar Proteome 47 A. General Aspects of Comparative Proteomics at the Subcellular Level 47 B. Examples of Comparative Proteome Analysis at the Subcellular Level 47 1. Monitoring of Dynamic Changes in Single Distinct Subcellular Structures 47 a. Microsomes 47 b. Phagosomes 48 c. Lipid rafts 48 d. Proteome analysis approaches to the ananlysis of synptic plasticty 48 2. Monitoring Protein Translocation 48 a. Changes in subcellular proteomes associated with apoptosis 48 b. Nucleolus: Proteome alterations because of inhibition of protein synthesis 49 VI. Molecular Biology‐Based Approaches in Subcellular Proteomics 49 VII. Concluding Remarks 52 Acknowledgments 52 Abbreviations 52 References 52 The step from the analysis of the genome to the analysis of the proteome is not just a matter of numerical complexity in terms of variants of gene products that can arise from a single gene. A significant further level of complexity is introduced by the supramolecular organization of gene products because of protein–protein interactions or targeting of proteins to specific subcellular structures. There is currently no single proteome analysis strategy that can sufficiently address all levels of the organization of the proteome. To approach an appropriate analytical complement for the interrogation of the proteome at all of the levels at which it is organized, there emerges the need for a whole arsenal of proteomics strategies. The proteome analysis at the level of subcellular structures (that can be enriched by subcellular fractionation) represents an analytical strategy that combines classic biochemical fractionation methods and tools for the comprehensive identification of proteins. Among the key potentials of this strategy is the capability to screen not only for previously unknown gene products but also to assign them, along with other known, but poorly characterized gene products, to particular subcellular structures. Furthermore, the analysis at the subcellular level is a prerequisite for the detection of important regulatory events such as protein translocation in comparative studies. This review is meant to give an overview on recent key studies in the field of proteome analysis at the level of subcellular structures, and to highlight potentials and requirements. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 22:27–56, 2003; Published online in Wiley InterScience ( www.interscience.wiley.com)