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Ten Years of the Proteome |
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1 | (14) |
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Introduction to the Proteome |
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1 | (2) |
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2 | (1) |
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Could Things Have Been Different? |
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3 | (1) |
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Proteomics Is Technology-Driven |
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3 | (5) |
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3 | (2) |
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5 | (1) |
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Making Sense of All the Data |
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6 | (2) |
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What Has Proteomics Delivered? |
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8 | (1) |
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9 | (2) |
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This Book and Some Conclusions |
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11 | (4) |
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11 | (4) |
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Sample Preparation and Prefractionation Techniques for Electrophoresis-Based Proteomics |
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15 | (26) |
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15 | (1) |
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Conventional Sample Preparation |
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16 | (2) |
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18 | (4) |
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Cysteine Chemistry - Reduction and Alkylation |
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18 | (1) |
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Cysteine Chemistry - β-Elimination |
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19 | (1) |
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Lysine Chemistry - Carbamylation |
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20 | (2) |
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Multiplexed Approaches to Proteomics |
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22 | (2) |
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24 | (6) |
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Fractional Centrifugation |
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24 | (1) |
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Chromatographic Techniques |
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25 | (1) |
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General Chromatographic Methods |
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25 | (1) |
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Sample Fractionation with Stacked Sorbents |
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26 | (1) |
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Electrophoresis-Based Methods |
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26 | (1) |
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Continuous Electrophoresis in Free Liquid Films |
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27 | (1) |
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Rotationally Stabilised Focusing Apparatus: the Rotofor |
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28 | (1) |
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Sample Prefractionation via Multicompartment Electrolysers with Isoelectric Membranes |
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28 | (2) |
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Miniaturised Isoelectric Separation Devices |
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30 | (1) |
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Other Methods for Prefractionation of Samples |
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30 | (5) |
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Depletion of High-Abundance Proteins |
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30 | (1) |
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Equaliser Beads: the Democratic Versus the Plutocratic Proteome |
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31 | (4) |
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35 | (6) |
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36 | (5) |
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Protein Identification in Proteomics |
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41 | (28) |
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41 | (1) |
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Attributes of Proteins Useful for Their Identification |
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42 | (3) |
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42 | (1) |
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Protein Isoelectric Point |
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42 | (1) |
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42 | (1) |
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Partial Sequence or Sequence Tag |
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43 | (1) |
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Protein Amino Acid Composition |
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43 | (2) |
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Protein Identification by Mass Spectrometry |
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45 | (20) |
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`Top-Down' Versus `Bottom-Up' Strategies for Protein Identification |
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45 | (2) |
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Introduction to Mass Spectrometry |
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47 | (1) |
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47 | (1) |
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48 | (2) |
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50 | (1) |
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Protein Identification by Peptide Mass Fingerprinting |
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51 | (1) |
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51 | (2) |
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Identification and Characterisation of Modified Peptides by Peptide Mass Fingerprinting |
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53 | (2) |
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Limitations of Peptide Mass Fingerprinting |
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55 | (1) |
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Tandem Mass Spectrometry Based Identification |
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56 | (1) |
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Tandem Mass Spectrometry Spectra |
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56 | (1) |
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The `Peptide Fragment Fingerprinting' Approach |
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57 | (3) |
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60 | (1) |
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Identification and Characterisation of Peptides with Unexpected Modifications |
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61 | (1) |
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Spectral Library Searches |
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62 | (3) |
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65 | (1) |
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65 | (4) |
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66 | (3) |
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Quantitation in Proteomics |
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69 | (26) |
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69 | (1) |
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Non-mass-spectrometric Approaches to Quantitation |
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70 | (4) |
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Relative Quantitation by Mass Spectrometry |
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74 | (9) |
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Absolute or Relative Quantitation? |
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76 | (1) |
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Introduction of Stable Isotopes Using Chemical Tags |
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76 | (4) |
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Enzyme-Mediated Incorporation of Stable Isotopes |
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80 | (1) |
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Biological Incorporation of Stable Isotopes by Metabolic Labelling |
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81 | (1) |
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Relative Quantitation Without Use of Stable Isotope Labelling |
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82 | (1) |
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Absolute Quantitation by Mass Spectrometry |
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82 | (1) |
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Analysis of Known Post-translational Modifications |
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83 | (4) |
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83 | (2) |
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85 | (2) |
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87 | (1) |
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87 | (8) |
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88 | (7) |
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95 | (28) |
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95 | (4) |
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An Overview of Modifications: What Are They and Where Do They Occur? |
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99 | (1) |
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How Do We Find Post-translational Modifications? |
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100 | (5) |
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100 | (2) |
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Detection of Co- and Post-translational Modifications |
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102 | (1) |
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Strategy for the Analysis of Modifications: Top Down Versus Bottom Up |
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103 | (1) |
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Mass Spectrometry for Analysis of Co- and Post-translational Modifications |
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104 | (1) |
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Analysis of Specific Modifications |
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105 | (4) |
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106 | (1) |
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106 | (1) |
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Ubiquitination and Sumoylation |
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107 | (1) |
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107 | (2) |
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The Function of Protein Post-translational Modifications: More Than Meets the Eye? |
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109 | (2) |
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Some Interesting Modification Stories |
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111 | (5) |
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111 | (2) |
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The Apolipoprotein E Story |
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113 | (1) |
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114 | (1) |
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115 | (1) |
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116 | (7) |
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116 | (7) |
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123 | (22) |
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Catherine G. Zimmermann-Ivol |
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123 | (1) |
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Image Analysis of Two-Dimensional Electrophoresis Gels |
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124 | (6) |
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First Steps in Gel Image Analysis |
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125 | (2) |
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Applications to Different Proteomics Approaches |
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127 | (1) |
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128 | (1) |
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128 | (1) |
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Two-Dimensional Difference Gel Electrophoresis |
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128 | (2) |
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Liquid Chromatography-Mass Spectrometry |
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130 | (4) |
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First Steps in Liquid Chromatography-Mass Spectrometry Image Analysis |
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130 | (1) |
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Applications to Different Proteomics Approaches |
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131 | (1) |
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Monitoring Experiments and Post-translational Modifications |
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131 | (1) |
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132 | (2) |
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134 | (4) |
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Imaging Mass Spectrometry |
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138 | (3) |
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Imaging Mass Spectrometry - Technical Aspects |
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139 | (1) |
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Imaging Mass Spectrometry - Applications |
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140 | (1) |
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141 | (4) |
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142 | (3) |
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Data Integration in Proteomics |
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145 | (24) |
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145 | (3) |
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Integration As Gathering and Cross-Linking Information |
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148 | (11) |
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Selection of Sources and Quantification |
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148 | (1) |
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148 | (1) |
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149 | (1) |
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Biology Inspired Cross-Linking |
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150 | (1) |
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The UniProt Universal Protein Knowledgebase |
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150 | (2) |
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152 | (1) |
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Integrating Elements of the Proteomics Workflow |
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153 | (1) |
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High-Throughput Data: Standards and Repositories |
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153 | (1) |
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154 | (1) |
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PeptideAtlas and the Global Proteome Machine |
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155 | (1) |
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156 | (1) |
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Integration As a Federated Effort |
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156 | (1) |
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156 | (2) |
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158 | (1) |
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Integration As Blending of Information |
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159 | (5) |
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159 | (1) |
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160 | (1) |
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Examples of Visualisation Tools Merging Several Sources |
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161 | (1) |
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From Data Integration to Systems Biology |
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162 | (2) |
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164 | (5) |
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164 | (5) |
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Protein-Protein Interactions |
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169 | (24) |
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169 | (1) |
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Protein-Protein Interactions in Human Diseases: Altered Protein Connectivity Leads to Disorder |
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170 | (2) |
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Charting Protein-Protein Interactions |
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172 | (9) |
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Characterisation of All Coding Sequences in an Organism |
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175 | (1) |
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Monitoring Binary Interactions: the Yeast Two-Hybrid System |
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175 | (2) |
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Analysis of Protein Complexes by Affinity Purification and Mass Spectrometry |
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177 | (3) |
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Luminescence-Based Mammalian Interactome Mapping |
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180 | (1) |
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180 | (1) |
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180 | (1) |
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Biological and Biomedical Applications |
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181 | (5) |
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Charting of Diseases and Pharmacologically Relevant Pathways |
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181 | (1) |
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Lessons Learned from Global Interaction Analyses in Yeast |
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182 | (2) |
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An Emerging Application: the Development of Small-Molecule Protein-Protein Interaction Inhibitors |
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184 | (2) |
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186 | (7) |
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187 | (6) |
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Biomedical Applications of Proteomics |
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193 | (30) |
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193 | (1) |
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The Application of Proteomics to Medicine |
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194 | (2) |
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Disease Diagnosis from Body Fluids |
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196 | (1) |
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197 | (5) |
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197 | (1) |
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Application of Proteomics to Vascular Diseases and Atherosclerosis |
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198 | (1) |
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Application of Proteomics to Cardiovascular Diseases |
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199 | (1) |
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Application of Proteomics to Cerebrovascular Disease |
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200 | (1) |
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201 | (1) |
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Neurodegenerative Disorders |
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202 | (4) |
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202 | (1) |
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Proteomic Profiling of Neurodegenerative Disorders |
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203 | (2) |
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Cerebrospinal Fluid Protein Markers |
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205 | (1) |
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206 | (5) |
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Biomarker Discovery in Cancer Proteomics |
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207 | (1) |
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207 | (1) |
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Primary and Established Cell Lines |
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208 | (1) |
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Proteomic Profiling in Oncology |
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209 | (1) |
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Surface-Enhanced Laser Desorption/Ionisation Time-of-Flight Mass Spectrometry |
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210 | (1) |
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210 | (1) |
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Tissue Profiling by Matrix-Assisted Laser Desoprtioon/Ionisation Mass Spectrometry Imaging |
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210 | (1) |
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Use of Proteomics To Define the Tissue of Origin |
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211 | (1) |
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211 | (1) |
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Toxicopharmacology: the Example of Type 2 Diabetes |
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211 | (4) |
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212 | (1) |
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Pathogenesis of Type 2 Diabetes |
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212 | (1) |
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Treatments of Type 2 Diabetes |
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213 | (1) |
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Proteomics for the Discovery of Treatment Targets for Type 2 Diabetes |
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213 | (2) |
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Current Limitations and Future Directions of Proteomics for Medicine |
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215 | (2) |
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215 | (1) |
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216 | (1) |
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217 | (1) |
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Present and Future Directions |
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217 | (6) |
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217 | (6) |
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Proteomics: Where to Next? |
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223 | (8) |
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223 | (1) |
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The Relevance of -omics to Biology |
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224 | (1) |
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Technological Developments in Proteomics |
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225 | (2) |
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Characterising Modifications |
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226 | (1) |
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226 | (1) |
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The Next Steps for Proteomics: Diagnostics and Drugs |
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227 | (2) |
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228 | (1) |
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228 | (1) |
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229 | (2) |
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229 | (2) |
| Index |
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231 | |
Lisainfo e-raamatute kohta