Identification of protein associations in organelles, using mass spectrometry‐based proteomics

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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 b6f 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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