Abstract
| I. | Introduction | 232 |
| II. | Proteomic Analysis | 233 |
| | A. Sample Preparation | 233 |
| | B. Two‐Dimensional (2‐D) Electrophoresis | 234 |
| | C. Protein Quantification | 235 |
| | D. Mass Spectrometry (MS) | 236 |
| | 1. Matrix‐Assisted Laser Desorption/Ionization Time‐of‐Flight Mass Spectroscopy (MALDI‐TOF‐MS) | 236 |
| | 2. Tandem MS | 237 |
| III. | 2‐D Brain Protein Databases | 238 |
| | A. Database Construction | 238 |
| | B. Subcellular Location | 240 |
| | C. Frequency of Detection | 240 |
| | D. Protein Function | 242 |
| IV. | Alterations in the Protein Levels | 243 |
| | A. Adult Brain | 243 |
| | B. Fetal Brain | 245 |
| V. | Proteomic Studies on Rat Brain | 245 |
| | A. Differences Between Neonatal and Adult Brain | 245 |
| | B. Post‐Mortem Changes | 248 |
| | C. Toxicology Studies | 248 |
| VI. | Limitations | 248 |
| | A. Brain Samples | 248 |
| | B. Protein Detection in 2‐D Gels | 249 |
| | 1. Low‐Abundance Proteins | 249 |
| | 2. Hydrophobic Proteins | 250 |
| | 3. Acidic and Basic Proteins | 251 |
| | 4. Low‐ and High‐Molecular Mass Proteins | 251 |
| | 5. Protein Heterogeneity | 251 |
| | C. Protein Indentification | 252 |
| VII. | Perspectives | 253 |
| VIII. | Conclusions | 253 |
| Acknowledgments | 254 |
| References | 254 |
Approximately 30–50% of the genes in mammals are expressed in the nervous system. A differential expression of genes in distinct patterns is necessary for the generation of the large variety of neuronal phenotypes. Proteomic analysis of brain compartments may be useful to understand the complexity, to investigate disorders of the central nervous system, and to search for corresponding early markers. Up to now, proteomics has mainly studied the identity and levels of the abundant human, rat, and mouse brain proteins as well as changes of their levels and the modifications that result from various neurological disorders, like Alzheimer's disease and Down's syndrome in humans and in animal models of those diseases. The proteins, for which altered levels in these disorders have been observed, exert mainly neurotransmission, guidance, and signal‐transduction functions, or are involved in detoxification, metabolism, and conformational changes. Some of those proteins may be potential drug targets. Further improvement of proteomics technologies to increase sensitivity and efficiency of detection of certain protein classes is necessary for a more detailed analysis of the brain proteome. In this review, a description of the proteomics technologies applied in the investigation of the brain, the major findings that resulted from their application, and the potential and limitations of the current technologies are discussed. © 2004 Wiley Periodicals, Inc., Mass Spec Rev 23:231–258, 2004