Abstract
| βI. | 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 |
| | ββA. ProteinβIdentification Strategies Successfully Used in Subcellular Proteomics | 30 |
| | ββB. Subcellular Fractionation | 31 |
| | ββC. Strategies to Validate Subcellular Proteomics Data | 33 |
| IV. | Examples of Subcellular Proteome Mapping Studies | 34 |
| | ββA. Functional Architecture of the Nucleus | 34 |
| | βββ1. Nuclear Envelope (NE) | 34 |
| | βββ2. Nuclear Pore Complex (NPC) | 35 |
| | βββ3. Interchromatin Granule Clusters | 40 |
| | βββ4. Nucleous | 40 |
| | βββ5. Other Subnuclear Structures | 40 |
| | ββB. Proteomic Analysis of Small Organelles and Vesicles | 41 |
| | βββ1. Golgi Apparatus | 41 |
| | βββ2. Mitochondria | 41 |
| | βββ3. Chloroplasts | 42 |
| | βββ4. Peroxisomes | 43 |
| | βββ5. Other Organelles | 44 |
| | ββC. Subcellular Proteomics at the Level of TissueβSpecific Structures: the Synapse | 44 |
| V. | Monitoring Dynamic Changes in the Subcellullar Proteome | 47 |
| | ββA. General Aspects of Comparative Proteomics at the Subcellular Level | 47 |
| | ββB. Examples of Comparative Proteome Analysis at the Subcellular Level | 47 |
| | βββ1. Monitoring of Dynamic Changes in Single Distinct Subcellular Structures | 47 |
| | ββββa. Microsomes | 47 |
| | ββββb. Phagosomes | 48 |
| | ββββc. Lipid rafts | 48 |
| | ββββd. Proteome analysis approaches to the ananlysis of synptic plasticty | 48 |
| | βββ2. Monitoring Protein Translocation | 48 |
| | ββββa. Changes in subcellular proteomes associated with apoptosis | 48 |
| | ββββb. Nucleolus: Proteome alterations because of inhibition of protein synthesis | 49 |
| VI. | Molecular BiologyβBased 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 proteinβprotein 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. Β© 2003 Wiley Periodicals, Inc., Mass Spec Rev 22:27β56, 2003; Published online in Wiley InterScience (www.interscience.wiley.com)