✍ Scribed by Dale E. Warnock; Eoin Fahy; Steven W. Taylor
No coin nor oath required. For personal study only.
| I. | Introduction | 260 |
| II. | Progress on Mapping Organellar Proteomes and Their Component Protein Complexes | 260 |
| | A. Mitochondria | 260 |
| | 1. Global Analysis | 260 |
| | 2. Directed Analysis | 262 |
| | 3. Protein Complexes | 263 |
| | a. Complex V | 263 |
| | b. Complex I | 264 |
| | c. Mitochondrial ribosomal complexes | 264 |
| | d. Other mitochondrial complexes | 265 |
| | B. Chloroplasts | 265 |
| | 1. Directed Analysis | 265 |
| | 2. Protein Complexes | 266 |
| | a. Photosystems I and II antenna proteins | 266 |
| | b. Cytochrome b~6~f complex | 266 |
| | c. Chloroplast ribosomal complexes | 267 |
| | C. Golgi Apparatus | 267 |
| | 1. Global Analysis | 267 |
| | 2. Protein Complexes | 267 |
| | a. Triton X‐100 insoluble fraction | 268 |
| | D. Lysosomes, Peroxisomes, Phagosomes, and Lysosome‐Related Organelles (LROs) | 268 |
| | 1. Global Analysis | 268 |
| | a. Lysosomes | 268 |
| | b. Peroxisomes | 269 |
| | c. Phagosomes | 269 |
| | d. LROs | 269 |
| | 2. Protein Complexes | 270 |
| | a. Lipid rafts of the endosome/lysosome system | 270 |
| | E. Nucleolus | 270 |
| | 1. Directed Analysis | 270 |
| | 2. Protein Complexes | 271 |
| | a. Nucleolus | 271 |
| | b. Nuclear‐pore complex | 271 |
| | c. Pol II preinitiation complex (PIC) | 271 |
| III. | Organellar Bioinformatics | 272 |
| | A. Prediction Strategies | 272 |
| | B. Protein–Protein Interaction Databases | 274 |
| IV. | Validation | 274 |
| V. | Concluding Remarks | 276 |
| Abbreviations | 276 |
| Acknowledgments | 277 |
| References | 277 |
Recent literature that highlights the power of using mass spectrometry (MS) for protein identification from preparations of highly purified organelles and other large subcellular structures is covered in this review with an emphasis on techniques that preserve the integrity of the functional protein complexes. Recent advances in distinguishing contaminant proteins from “bonafide” organelle‐localized proteins and the affinity capture of protein complexes are reviewed, as well as bioinformatic strategies to predict protein organellar localization and to integrate protein–protein interaction maps obtained from MS‐affinity capture methods with data obtained from other techniques. Those developments demonstrate that a revolution in cellular biology, fueled by technical advances in MS‐based proteomic techniques, is well underway. © 2004 Wiley Periodicals, Inc., Mass Spec Rev 23:259–280, 2004
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