Subcellular proteomics
Authors: Dreger Mathias 
Published: May 2003

Abstract I.Introduction: The Need for a Repertoire of Proteome Analysis Strategies as the Analytical Complement28II.Rationale of Proteome Analysis at the Level of Subcellular Structures29III.Analytical Tools in Subcellular Proteomics29  A. Protein‐Identification Strategies Successfully Used in Subcellular Proteomics30  B. Subcellular Fractionation31  C. Strategies to Validate Subcellular Proteomics Data33IV.Examples of Subcellular Proteome Mapping Studies34  A. Functional Architecture of the Nucleus34   1. Nuclear Envelope (NE)34   2. Nuclear Pore Complex (NPC)35   3. Interchromatin Granule Clusters40   4. Nucleous40   5. Other Subnuclear Structures40  B. Proteomic Analysis of Small Organelles and Vesicles41   1. Golgi Apparatus41   2. Mitochondria41   3. Chloroplasts42   4. Peroxisomes43   5. Other Organelles44  C. Subcellular Proteomics at the Level of Tissue‐Specific Structures: the Synapse44V.Monitoring Dynamic Changes in the Subcellullar Proteome47  A. General Aspects of Comparative Proteomics at the Subcellular Level47  B. Examples of Comparative Proteome Analysis at the Subcellular Level47   1. Monitoring of Dynamic Changes in Single Distinct Subcellular Structures47    a. Microsomes47    b. Phagosomes48    c. Lipid rafts48    d. Proteome analysis approaches to the ananlysis of synptic plasticty48   2. Monitoring Protein Translocation48    a. Changes in subcellular proteomes associated with apoptosis48    b. Nucleolus: Proteome alterations because of inhibition of protein synthesis49VI.Molecular Biology‐Based Approaches in Subcellular Proteomics49VII.Concluding Remarks52Acknowledgments52Abbreviations52References52The 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)