Introduction |
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vii | |
1 Overview of Proteomics |
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1 | |
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1 | |
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1-2 Establishment of Proteomics Using Mass Spectrometry, |
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3 | |
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1-2-1 Protein Separations by Two-Dimensional Electrophoresis, |
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3 | |
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1-2-2 Development of the Technologies for Protein Identification, |
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5 | |
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1-2-3 Protein Identification Based on Gel Separation and Mass Spectrometry, |
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6 | |
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1-3 Strategies for Characterizing Proteomes and Understanding Proteome Function, |
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15 | |
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1-3-1 Modification-Specific Proteomics, |
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17 | |
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1-3-2 Activity-Based Protein Profiling/Enzyme Substrate Proteomics, |
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31 | |
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1-3-3 Subcellular (Organellar) Proteomics, |
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41 | |
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1-3-4 Machinery or Complex Interaction Proteomics, |
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45 | |
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1-3-5 Dynamic Proteomics, |
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46 | |
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49 | |
2 Proteomic Tools for Analysis of Cellular Dynamics |
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63 | |
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2-1 LC-Based Proteomics Technologies, |
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63 | |
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2-1-1 LC-MS system for Peptide Separation and Identification, |
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71 | |
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2-1-2 Application of LC-MS Methods to Functional Proteomics, |
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101 | |
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2-2 Development of Quantitative Proteomics, |
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131 | |
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2-2-1 Isotope Labeling for Quantitative Analysis Using MS, |
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132 | |
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2-2-2 Quantification Strategy for LC-MS Analysis of Isotope-Labeled Peptide Mixture and Software for Computer Analysis, |
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140 | |
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2-2-3 Label-Free Quantification Software, |
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145 | |
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2-2-4 Absolute Quantification, |
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147 | |
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153 | |
3 Dynamics of Functional Cellular Machinery: From Statics to Dynamics in Proteomic Biology |
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167 | |
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3-1 Dynamic Analysis of Cellular Function, |
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167 | |
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3-1-1 Strategy for Dynamic Analysis of Cellular Machinery (Multiprotein Complexes), |
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168 | |
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3-1-2 Methods for the Isolation of a Cellular Machine/Multiprotein Complex, |
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174 | |
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3-1-3 Cellular Machinery (Multiprotein Complex), |
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196 | |
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3-2 Dynamics of Ribosome Biogenesis, |
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198 | |
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3-2-1 Snapshot Analysis of Preribosomal Particles in Yeast, |
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201 | |
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3-2-2 Snapshot Analysis of Preribosomal Particles in Mammals, |
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207 | |
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3-2-3 Quantitative (Dynamic) Analysis Using Isotope-Labeled Reagents, |
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224 | |
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3-2-4 Outline of Human/Mammalian Ribosome Biogenesis, |
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231 | |
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3-3 Dynamic Analysis of Subcellular Structures, |
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232 | |
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3-3-1 Proteome Dynamics of the Nucleolus, |
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233 | |
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236 | |
Index |
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249 | |