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Part I Sample Preparation |
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Applications of Pressure Cycling Technology (PCT) in Proteomics |
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3 | (16) |
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3 | (2) |
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Sample Preparation by the PCT SPS Compared to Traditional Methods |
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5 | (3) |
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Potential Mechanisms of Action of PCT |
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8 | (1) |
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PCT and Protein Stability |
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9 | (1) |
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PCT and the Role of Extraction Buffers |
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10 | (1) |
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Examples of Protein Extraction Using the PCT SPS |
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11 | (4) |
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15 | (4) |
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17 | (2) |
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Applications of Ion-Exchange (IEX) Chromatography to Reduce Sample Complexity Prior to Two-Dimensional Gel Electrophoresis (2DE) |
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19 | (10) |
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19 | (1) |
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IEX Chromatography Basics |
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20 | (2) |
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20 | (1) |
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IEX Chromatography Media Available |
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20 | (1) |
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Illustration of IEX Chromatography Separation Correlated with 2DE |
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21 | (1) |
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Applications of IEX Chromatography Prior to 2DE Analysis |
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22 | (5) |
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Fractionation of Human Plasma |
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22 | (1) |
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Impact on IEX Prefractionation on Resolution in 2DE |
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23 | (4) |
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27 | (2) |
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27 | (2) |
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Separations in Proteomics: Use of Camelid Antibody Fragments in the Depletion and Enrichment of Human Plasma Proteins for Proteomics Applications |
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29 | (12) |
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30 | (1) |
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Heavy-Chain Antibodies from the Camelid Family |
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31 | (1) |
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Roadmap to Llama Antibodies |
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31 | (7) |
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Stage 1: Immunization of Llamas and Creation of the VHH Library |
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32 | (1) |
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Stage 2: Screening for Antigen-Binding VHH Fragments |
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32 | (1) |
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Stage 2: Screening for the Ultimate Ligand |
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32 | (1) |
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Stage 3: Ligand Production |
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33 | (1) |
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Stage 3: Coupling to Matrices |
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33 | (2) |
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Stage 3: Depletion of HSA and Human IgG from Human Plasma |
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35 | (3) |
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38 | (3) |
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38 | (1) |
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38 | (3) |
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Novel Plasma Protein Separation Strategy Using Multiple Avian IgY Antibodies for Proteomic Analysis |
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41 | (22) |
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42 | (2) |
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44 | (2) |
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Coupling of Affinity-Purified IgY to UltraLink® Hydrazide Gel |
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44 | (1) |
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Spin Column Method for Removal of Serum and Plasma Abundant Protein |
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44 | (1) |
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Albumin Depletion with Liquid Chromatography Workstation |
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44 | (1) |
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One-Dimensional Electrophoresis |
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45 | (1) |
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Two-Dimensional Electrophoresis |
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45 | (1) |
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Protein Digestion and MALDI Analysis |
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45 | (1) |
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Bioinformatic Database Search |
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45 | (1) |
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46 | (7) |
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Cibacron Blue Depletion of Rat Albumin Removed Many Nontarget Proteins |
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46 | (1) |
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Structural Comparisons of IgG and IgY and Their Covalent Coupling to Microbead Carriers |
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46 | (2) |
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IgY Gels Have High Capacity and Specificity |
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48 | (1) |
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Anti-HSA IgY Gels Have Excellent Cross-Reactivity to Various Mammalian Albumins |
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48 | (1) |
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IgYs Cross-React and Are Also Effective at Separating IgG, Fibrinogen, and Transferrin from Human and Rat Plasma |
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49 | (1) |
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Six Abundant Plasma Proteins Are Effectively Removed by MIXED6 IgY Gels |
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50 | (2) |
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High-Throughput Proteomic Sample Processing Is Facilitated by Use of FPLC Techniques |
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52 | (1) |
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53 | (10) |
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60 | (1) |
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60 | (3) |
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Immunoaffinity Depletion of High-Abundant Proteins for Proteomic Sample Preparation |
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63 | (18) |
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64 | (2) |
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66 | (5) |
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66 | (1) |
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Sample Collection and Processing |
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67 | (1) |
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67 | (1) |
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Immunoaffinity Separation |
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67 | (1) |
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Analysis of Flow-Through Fractions by Enzyme-Linked Immunosorbent Assay (ELISA) |
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68 | (1) |
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Processing of Depleted Serum and Bound Fractions for Down-Stream Analysis |
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69 | (1) |
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One-Dimensional (1D) and Two-Dimensional (2D) Gel Electrophoresis |
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69 | (1) |
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Liquid Chromatography--Tandem Mass Spectrometry (LC-MS/MS) |
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69 | (1) |
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70 | (1) |
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Analysis of Cibacron Blue Bound Fraction |
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70 | (1) |
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Analysis of Cibacron Blue Flow-Through Fraction |
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71 | (1) |
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71 | (6) |
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Immunoaffinity Column Performance and Reproducibility |
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71 | (1) |
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Completeness of the Depletion of High-Abundant Proteins |
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71 | (2) |
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Specificity of the Immunodepletion |
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73 | (4) |
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77 | (4) |
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78 | (3) |
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Isolation of Plasma Membrane Proteins for Proteomic Analysis |
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81 | (8) |
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81 | (1) |
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Preparation of the Plasma Membrane Fraction |
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82 | (2) |
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82 | (1) |
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82 | (1) |
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Cells Growing in Monolayers |
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83 | (1) |
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84 | (1) |
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85 | (4) |
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86 | (1) |
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86 | (3) |
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New Ultrafiltration and Solid Phase Extraction Techniques Improve Serum Peptide Detection |
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89 | (18) |
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89 | (2) |
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91 | (2) |
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Preparation of Serum Peptides by UF and SPE |
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91 | (1) |
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Preparation of Serum Peptides by Acetonitrile Precipitation |
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92 | (1) |
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Peptide Analysis by Mass Spectrometry |
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93 | (1) |
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Two-Dimensional (2D) Gel Electrophoresis |
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93 | (1) |
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93 | (4) |
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97 | (10) |
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98 | (9) |
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Part II Sample Prefractionation and Analysis |
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Tools for Sample Preparation and Prefractionation in Two-Dimensional (2D) Gel Electrophoresis |
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107 | (28) |
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108 | (1) |
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Sample Preparation Basics |
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109 | (10) |
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109 | (2) |
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Sample and Lysis Buffer Constituents |
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111 | (1) |
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111 | (1) |
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112 | (1) |
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113 | (1) |
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114 | (1) |
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General Solubilization Cocktails and Sample Preparation Guidelines |
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114 | (1) |
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Technologies for Protein Sample Preparation |
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115 | (1) |
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115 | (2) |
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117 | (1) |
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118 | (1) |
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General-Purpose Cleanup for Improved Resolution and Reproducibility |
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119 | (3) |
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Removal of Interfering Contaminants |
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119 | (1) |
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120 | (1) |
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120 | (1) |
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121 | (1) |
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121 | (1) |
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121 | (1) |
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Removal of Disulfide Bonds |
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122 | (1) |
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Fractionation: The Quest for Low-Abundance Proteins |
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122 | (5) |
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Fractionation by Subcellular Location |
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123 | (1) |
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Fractionation by Differential Solubility |
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123 | (1) |
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Fractionation by Protein Size |
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124 | (1) |
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Fractionation by Charge and pI |
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124 | (1) |
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125 | (1) |
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Multicompartment Electrolyzers |
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126 | (1) |
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Off-Gel IEF in Multicompartment Devices |
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127 | (1) |
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Continuous Free-Flow Electrophoresis (FFE) |
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127 | (1) |
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127 | (1) |
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127 | (8) |
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128 | (7) |
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Optic Nerve Fractionation for Proteomics |
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135 | (22) |
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135 | (1) |
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136 | (2) |
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136 | (1) |
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Optic Nerve Sample Preparation |
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136 | (1) |
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137 | (1) |
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137 | (1) |
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138 | (1) |
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138 | (1) |
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138 | (14) |
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Extraction of Protein from Optic Nerve |
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138 | (3) |
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Optic Nerve IEF Using the Multicompartment Electrolyzer |
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141 | (1) |
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Identification of Optic Nerve Proteins following MCE Fractionation |
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142 | (10) |
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152 | (5) |
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153 | (1) |
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153 | (4) |
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Fractionation of Retina for Proteomic Analyses |
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157 | (30) |
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Kutralanathan Renganathan |
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157 | (1) |
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158 | (2) |
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Bovine Retina Sample Preparation |
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158 | (1) |
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Western Blot Analysis and 1D Electrophoresis |
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159 | (1) |
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159 | (1) |
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159 | (1) |
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159 | (1) |
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160 | (21) |
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Comparison of Detergent Extracts of Bovine Retina |
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160 | (1) |
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Retina Fractionation by Solution-State IEF and 1D Page |
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160 | (3) |
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163 | (18) |
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181 | (6) |
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183 | (1) |
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183 | (4) |
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Reducing Protein Sample Complexity with Free Flow Electrophoresis (FFE) |
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187 | (20) |
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187 | (1) |
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Principle of Free Flow Electrophoresis |
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188 | (3) |
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191 | (3) |
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191 | (1) |
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192 | (1) |
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192 | (1) |
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193 | (1) |
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Post-FFE Treatment of Fractions |
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193 | (1) |
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194 | (8) |
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Liver Proteome Fractionation |
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194 | (2) |
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Plasma Proteome Fractionation |
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196 | (6) |
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202 | (5) |
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203 | (4) |
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Part III Applications of Electrophoresis in Proteomics |
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Destreaking Strategies for Two-Dimensional Electrophoresis |
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207 | (12) |
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Two-dimensional Gel Electrophoresis (2DE) and Basic End Streaks |
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207 | (1) |
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Chemical Nature of Protein Streaking |
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208 | (1) |
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208 | (4) |
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Recent Advances in Destreaking Techniques |
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212 | (7) |
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216 | (3) |
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Proteomic Approaches to the Study of Rheumatoid Arthritis |
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219 | (16) |
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219 | (1) |
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220 | (1) |
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221 | (2) |
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Clinical Samples and Cell Culture |
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221 | (1) |
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Two-Dimensional Polyacrylamide Gel Electrophoresis (2D Page) Analysis of FLS |
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221 | (1) |
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Mass Spectrometry (MS) and Protein Identification |
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222 | (1) |
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MCE Fractionation of Synovial Fluid |
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222 | (1) |
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Chromatographic Separation |
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222 | (1) |
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SDS-Page of MCE Fractions |
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223 | (1) |
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223 | (1) |
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223 | (1) |
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223 | (8) |
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223 | (2) |
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Analysis of Synovial Fluid |
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225 | (6) |
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231 | (4) |
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231 | (4) |
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Immunoglobulin Patterns in Health and Disease |
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235 | (34) |
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236 | (1) |
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Immunoglobulins and Disorders |
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236 | (4) |
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236 | (1) |
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237 | (1) |
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237 | (1) |
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Waldenstrom's Macroglobulinemia |
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237 | (1) |
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238 | (1) |
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239 | (1) |
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239 | (1) |
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Monoclonal Gammopathy of Undetermined Significance |
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239 | (1) |
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240 | (1) |
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Methods to Investigate Immunoglobulin Patterns (as Exemplified for Serum) |
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240 | (2) |
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One-Dimensional Separations |
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240 | (1) |
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241 | (1) |
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242 | (1) |
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242 | (10) |
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242 | (2) |
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244 | (1) |
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244 | (4) |
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Biclonal and Oligoclonal Gammopathies |
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248 | (2) |
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250 | (2) |
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252 | (2) |
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Patterns of Healthy Individuals |
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252 | (1) |
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252 | (2) |
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Single-Chain Disregulations (in Serum and Urine) |
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254 | (3) |
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254 | (3) |
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257 | (1) |
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257 | (2) |
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Cerebrospinal Fluid (CSF) |
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257 | (1) |
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258 | (1) |
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Effusions and Lavage Fluids |
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259 | (1) |
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Conclusions and Perspectives |
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259 | (10) |
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259 | (10) |
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Difference Gel Electrophoresis (DIGE) |
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269 | (18) |
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270 | (3) |
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270 | (1) |
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271 | (1) |
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Of Proteomes and Dynamic Range of Expression |
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272 | (1) |
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273 | (1) |
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273 | (4) |
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274 | (1) |
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Recipes, Apparatus, and Chemicals for Sample Solubilization and Labeling |
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274 | (1) |
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274 | (1) |
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274 | (1) |
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275 | (1) |
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275 | (1) |
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275 | (1) |
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275 | (1) |
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275 | (1) |
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Sodium Dodecyl Sulfate--Polyacrylamide Gel Electrophoresis (SDS-Page) |
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275 | (1) |
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276 | (1) |
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276 | (1) |
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276 | (1) |
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Light Gradient Gel Solution |
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276 | (1) |
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Heavy Gradient Gel Solution |
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276 | (1) |
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277 | (1) |
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277 | (1) |
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277 | (1) |
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277 | (10) |
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277 | (1) |
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Introduction and General Notes |
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277 | (1) |
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278 | (1) |
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279 | (1) |
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279 | (1) |
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280 | (1) |
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Introduction and General Notes |
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280 | (1) |
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280 | (1) |
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Setting Up and Running the First Dimension |
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280 | (1) |
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Equilibration of IEF Gels |
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281 | (1) |
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281 | (1) |
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Assembling the Gel Cassettes |
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281 | (1) |
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Pouring the 10--15% Gradient Gels |
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282 | (1) |
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Setting Up and Running the Second Dimension |
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282 | (1) |
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Image Acquisition and Analysis |
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282 | (1) |
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Introduction and General Notes |
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282 | (1) |
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283 | (1) |
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284 | (1) |
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284 | (3) |
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Principles and Challenges of Basic Protein Separation by Two-Dimensional (2D) Electrophoresis |
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287 | (14) |
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287 | (1) |
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288 | (3) |
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288 | (1) |
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289 | (1) |
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Types of IPG Gels for 2D Electrophoresis |
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289 | (1) |
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289 | (1) |
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290 | (1) |
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290 | (1) |
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Overcoming Difficulties with Basic Protein Separations |
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291 | (5) |
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Instability of the Acrylamide Matrix |
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292 | (1) |
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Running Conditions for Basic IPG Strips |
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293 | (2) |
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Reduction and Alkylation Prior to 2D Electrophoresis |
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295 | (1) |
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296 | (5) |
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297 | (4) |
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Multidimensional Separation of Membrane Proteins |
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301 | (20) |
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301 | (2) |
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Integral Membrane Proteins |
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302 | (1) |
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Membrane-Associated Proteins |
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302 | (1) |
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The Need for Membrane Proteomics |
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302 | (1) |
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Classical Two-Dimensional Electrophoresis (2DE) Based Methods of Membrane Protein Isolation and Characterization |
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303 | (5) |
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Detergent Extraction Based Approaches |
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304 | (2) |
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Sequential Extraction Based Techniques |
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306 | (1) |
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Organic Solvent Based Extraction |
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307 | (1) |
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Membrane Stripping Procedures |
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308 | (1) |
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Liquid Chromatography Coupled with Mass Spectrometry Approaches |
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308 | (5) |
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1D LC-MS/MS Analysis Techniques |
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309 | (3) |
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Shotgun Proteomics: 2D LC-MS/MS Approaches |
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312 | (1) |
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Fungal Proteomics Examples |
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313 | (3) |
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316 | (5) |
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316 | (1) |
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317 | (4) |
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Structural Approaches in Glycoproteomics |
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321 | (24) |
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The Developing Field of Glycoproteomics |
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321 | (4) |
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Significance of Molecular Glycosylation |
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322 | (1) |
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322 | (3) |
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Separation by Two-Dimensional Gel Electrophoresis |
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325 | (1) |
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325 | (1) |
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326 | (1) |
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Glycoprotein Detection on 2D Gels |
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326 | (1) |
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326 | (1) |
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327 | (4) |
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327 | (1) |
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MS Profiles of Intact Glycoproteins: Top Down |
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328 | (1) |
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MS Profiles of Intact Glycoproteins: Bottom Up |
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329 | (1) |
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330 | (1) |
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Glycan Release Techniques |
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331 | (2) |
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332 | (1) |
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332 | (1) |
|
|
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333 | (1) |
|
Sequencing Released Glycans |
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333 | (12) |
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The Details of Glycan Structure by MSn |
|
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334 | (5) |
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339 | (6) |
|
Enrichment and Analysis of Glycoproteins in the Proteome |
|
|
345 | (18) |
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|
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|
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345 | (1) |
|
Lectin Affinity Chromatography |
|
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346 | (1) |
|
Boronate Affinity Chromatography |
|
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346 | (1) |
|
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347 | (5) |
|
Lectin Affinity Chromatography |
|
|
347 | (1) |
|
Boronate Affinity Chromatography |
|
|
348 | (1) |
|
|
|
348 | (1) |
|
Protein and Glycoprotein Staining |
|
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349 | (1) |
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349 | (1) |
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350 | (1) |
|
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350 | (1) |
|
N-Linked Oligosaccharides |
|
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351 | (1) |
|
O-Linked Oligosaccharides |
|
|
351 | (1) |
|
LC-ESI-MS of Oligosaccharides |
|
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351 | (1) |
|
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|
352 | (11) |
|
|
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358 | (5) |
|
Part IV Applications of High-Performance Liquid Chromatography |
|
|
|
Proteomic Analyses Using High-Efficiency Separations and Accurate Mass Measurements |
|
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363 | (24) |
|
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|
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|
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363 | (1) |
|
High-Throughput Approach for Global Proteomic Measurements |
|
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364 | (2) |
|
Essential Components for Effective LC-MS Proteomic Analysis |
|
|
366 | (10) |
|
Electrospray Ionization Efficiency |
|
|
367 | (2) |
|
High-Efficiency LC Separations |
|
|
369 | (2) |
|
Expanded Dynamic Range for MS |
|
|
371 | (1) |
|
Data Processing Components |
|
|
371 | (2) |
|
|
|
373 | (1) |
|
Peptide Identifications Using Accurate Mass and Time Measurements |
|
|
373 | (3) |
|
|
|
376 | (3) |
|
18O Stable-Isotope Labeling Techniques |
|
|
376 | (2) |
|
``Label-free'' Quantitation Using Intensity Information |
|
|
378 | (1) |
|
|
|
379 | (3) |
|
|
|
382 | (5) |
|
|
|
382 | (1) |
|
|
|
383 | (4) |
|
Middle-Out Proteomics: Incorporating Multidimensional Protein Fractionation and Intact Protein Mass Analysis as Elements of a Proteomic Workflow |
|
|
387 | (32) |
|
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|
|
|
|
|
|
|
|
|
388 | (4) |
|
|
|
388 | (2) |
|
|
|
390 | (1) |
|
Combining Top-Down and Bottom-Up Proteomics |
|
|
391 | (1) |
|
|
|
392 | (2) |
|
Ribosomal Protein Analysis |
|
|
392 | (1) |
|
Escherichia coli Analysis |
|
|
393 | (1) |
|
|
|
394 | (1) |
|
|
|
394 | (16) |
|
|
|
394 | (1) |
|
|
|
395 | (1) |
|
Mass Analysis of Intact Proteins |
|
|
395 | (2) |
|
Fractionation at the Intact Protein Level |
|
|
397 | (3) |
|
|
|
400 | (2) |
|
|
|
402 | (8) |
|
|
|
410 | (9) |
|
|
|
410 | (9) |
|
Polymeric Monolithic Capillary Columns in Proteomics |
|
|
419 | (20) |
|
|
|
Introduction and Overview |
|
|
419 | (2) |
|
High-Efficiency Peptide Analysis on Monolithic Multimode Capillary Columns |
|
|
421 | (4) |
|
High-Sensitivity ESI-MS Analysis of Protein Tryptic Digests Using Ultra Low I.D. Polystyrene-Divinylbenzene Monolithic Capillary Columns |
|
|
425 | (4) |
|
Polystyrene Monolithic Capillary Columns in On-Line 2D LC-ESI-MS Proteomic Analysis |
|
|
429 | (2) |
|
|
|
431 | (8) |
|
|
|
431 | (1) |
|
|
|
431 | (8) |
|
Part V Related Techniques |
|
|
|
Proteins Staining in Polyacrylamide Gels |
|
|
439 | (14) |
|
|
|
|
|
439 | (1) |
|
|
|
440 | (2) |
|
Staining Proteins with Tannins |
|
|
442 | (1) |
|
|
|
442 | (2) |
|
|
|
444 | (1) |
|
|
|
445 | (1) |
|
|
|
445 | (1) |
|
|
|
446 | (2) |
|
Recent Developments in Colloidal Coomassie Chemistry |
|
|
448 | (5) |
|
|
|
450 | (1) |
|
|
|
450 | (3) |
|
Multiplexed Proteomics: Fluorescent Detection of Proteins, Glycoproteins, and Phosphoproteins in Two-Dimensional (2D) Gels |
|
|
453 | (8) |
|
Birte Aggeler-Schulenberg |
|
|
|
|
453 | (1) |
|
|
|
454 | (3) |
|
|
|
454 | (1) |
|
Glycoprotein Detection Using Pro-Q Emerald 300 Glycoprotein Gel Stain |
|
|
455 | (1) |
|
Phosphoprotein Detection in 2D Gels |
|
|
455 | (1) |
|
Total Protein Detection Using SYPRO Ruby Protein Gel Stain |
|
|
456 | (1) |
|
Instrumentation for Imaging Fluorescent Stains and Data Analysis |
|
|
456 | (1) |
|
|
|
457 | (1) |
|
Detection of Phosphoproteins |
|
|
457 | (1) |
|
Detection of Glycoproteins |
|
|
458 | (1) |
|
Detection of Total Protein |
|
|
458 | (1) |
|
Three-Color Staining of Gels |
|
|
458 | (1) |
|
|
|
458 | (3) |
|
|
|
460 | (1) |
|
Glyoxyl Agarose and Its Composite Gels: Advantageous Alternatives to Polyacrylamide Gel Electrophoresis for Very Large and Small Proteins and Peptides and All Sizes in Between |
|
|
461 | (6) |
|
|
|
|
|
461 | (2) |
|
Preparation of Glyoxyl Agarose |
|
|
463 | (1) |
|
|
|
463 | (1) |
|
Simplified Immunoprobing with Compressed Gels |
|
|
463 | (1) |
|
Mass Production of the Composites |
|
|
464 | (1) |
|
|
|
464 | (1) |
|
|
|
464 | (3) |
|
|
|
464 | (3) |
|
Nuclear Magnetic Resonance--Driven Chemical Proteomics: The Functional and Mechanistic Complement to Proteomics |
|
|
467 | (22) |
|
|
|
|
|
|
|
468 | (1) |
|
|
|
468 | (5) |
|
Chemical Proteomics as Systems-Based Characterization of Protein Function |
|
|
468 | (1) |
|
NMR-Based Characterization of Protein Structure |
|
|
469 | (2) |
|
Protein Dynamics: From Snapshots to Movies |
|
|
471 | (1) |
|
NMR-Based Fragment Assembly: Modular Inhibitor Design in NMR Legoland™ |
|
|
471 | (1) |
|
The Emerging Role of NMR Spectroscopy in Chemical Proteomics |
|
|
472 | (1) |
|
Chemical Proteomic Applications of NMR In Vitro |
|
|
473 | (7) |
|
A NMR-Guided Design of Gene-Family-Focused Libraries of Chemical Proteomic Probes Using NMR Solve |
|
|
473 | (3) |
|
Cofactor Fingerprinting with STD NMR: Addressing the Needs of Functional Proteomics by Identifying Binding Preferences |
|
|
476 | (2) |
|
Ligand Docking Using NMR Constraints: T1 Relaxation or NOE Data |
|
|
478 | (2) |
|
Chemical Proteomic Applications of NMR In Vivo |
|
|
480 | (4) |
|
In Cell NMR: Chemical Proteomics in the Cellular Milieu |
|
|
480 | (1) |
|
Molecular Imaging: Magnetic Resonance Contrast Agents as Chemical Proteomic Probes in Whole Organisms |
|
|
481 | (3) |
|
|
|
484 | (5) |
|
|
|
484 | (5) |
|
Electrophoretic Nuclear Magnetic Resonance in Proteomics: Toward High-Throughput Structural Characterization of Biological Signaling Processes |
|
|
489 | (16) |
|
|
|
|
|
|
|
489 | (2) |
|
Separating Protein Signals without Physical Separation |
|
|
491 | (3) |
|
Structural Characterization of Coexisting Proteins in Solution |
|
|
494 | (1) |
|
Heat-Induced Convection in Biological Buffer Solutions |
|
|
495 | (4) |
|
High-Throughput Structural Determination of Protein Active Pockets |
|
|
499 | (2) |
|
|
|
501 | (4) |
|
|
|
502 | (1) |
|
|
|
502 | (3) |
| Index |
|
505 | |
