| Preface |
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vii | |
| Contributors |
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xiii | |
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Extraction and Solubilization of Proteins for Proteomic Studies |
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1 | (18) |
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Preparation of Bacterial Samples for 2-D Page |
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19 | (8) |
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Preparation of Yeast Samples for 2-D Page |
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27 | (4) |
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Preparation of Mammalian Tissue Samples for Two-Dimensional Electrophoresis |
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31 | (6) |
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Differential Detergent Fractionation of Eukaryotic Cells |
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37 | (12) |
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Serum or Plasma Sample Preparation for Two-Dimensional Gel Electrophoresis |
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49 | (6) |
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Preparation of Plant Protein Samples for 2-D Page |
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55 | (4) |
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Laser-Assisted Microdissection in Proteomic Analyses |
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59 | (8) |
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Purification of Cellular and Organelle Populations by Fluorescence-Activated Cell Sorting for Proteome Analysis |
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67 | (12) |
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Purification of Nucleoli From Lymphoma Cells and Solubilization of Nucleolar Proteins for 2-DE Separation |
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79 | (8) |
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Prefractionation of Complex Protein Mixture for 2-D Page Using Reversed-Phase Liquid Chromatography |
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87 | (10) |
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Fractionation of Complex Proteomes by Microscale Solution Isoelectrofocusing Using Zoom™ IEF Fractionators to Improve Protein Profiling |
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97 | (22) |
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Large-Format 2-D Polyacrylamide Gel Electrophoresis |
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119 | (14) |
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Analysis of Membrane Proteins by Two-Dimensional Gels |
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133 | (12) |
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2-D Page of High-Molecular-Mass Proteins |
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145 | (6) |
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Using Ultra-Zoom Gels for High-Resolution Two-Dimensional Polyacrylamide Gel Electrophoresis |
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151 | (16) |
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NEpHGE and pl Strip Proteomic 2-D Gel Electrophoretic Mapping of Lipid-Rich Membranes |
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167 | (10) |
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Silver Staining of 2-D Gels |
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177 | (8) |
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Zn2+ Reverse Staining Technique |
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185 | (8) |
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Multiplexed Proteomics Technology for the Fluorescence Detection of Glycoprotein Levels and Protein Expression Levels Using Pro-Q® Emerald and Sypro® Ruby Dyes |
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193 | (8) |
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Multiplexed Proteomics Technology for the Fluorescence Detection of Phosphorylation and Protein Expression Levels Using Pro-Q® Diamond and Sypro® Ruby Dyes |
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201 | (8) |
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Sensitive Quantitative Fluorescence Detection of Proteins in Gels Using Sypro® Ruby Protein Gel Stain |
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209 | (6) |
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Rapid, Sensitive Detection of Proteins in Minigels With Fluorescent Dyes: Coomassie Fluor Orange, Sypro® Orange, Sypro Red, and Sypro Tangerine Protein Gel Stains |
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215 | (8) |
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Differential In-Gel Electrophoresis in a High-Throughput Environment |
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223 | (16) |
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Statistical Analysis of 2-D Gel Patterns |
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239 | (20) |
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Francoise Seillier-Moiseiwitsch |
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2-DE Databases on the World Wide Web |
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259 | (8) |
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Computer Analysis of 2-D Images |
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267 | (12) |
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Comparing 2-D Electrophoretic Gels Across Internet Databases: An Open Source Application |
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279 | (28) |
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Sample Cleanup by Solid-Phase Extraction/Pipet-Tip Chromatography |
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307 | (4) |
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Protein Identification by In-Gel Digestion and Mass Spectrometric Analysis |
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311 | (4) |
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Peptide Sequences of 2-D Gel-Separated Protein Spots by Nanoelectrospray Tandem Mass Spectrometry |
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315 | (4) |
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Identification of Proteins by MALDI-TOF MS |
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319 | (6) |
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Sequencing of Tryptic Peptides Using Chemically Assisted Fragmentation and MALDI-PSD |
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325 | (16) |
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The In Situ Characterization of Membrane-Immobilized 2-D Page-Separated Proteins Using Ink-Jet Technology |
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341 | (14) |
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Protein Identification by Peptide Mass Fingerprinting |
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355 | (12) |
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Analysis of the Proteomes in Human Tissues by In-Gel Isoelectric Focusing and Mass Spectrometry |
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367 | (8) |
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Sarka Beranova-Giorgianni |
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Liquid Chromatography Coupled to MS for Proteome Analysis |
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375 | (10) |
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Quantitative Analysis of Proteomes and Subproteomes by Isotope-Coded Affinity Tags and Solid-Phase Glycoprotein Capture |
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385 | (8) |
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Amino Acid-Coded Mass Tagging for Quantitative Profiling of Differentially Expressed Proteins and Modifications in Cells |
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393 | (14) |
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Mass-Coded Abundance Tagging for Protein Identification and Relative Abundance Determination in Proteomic Experiments |
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407 | (10) |
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Virtual 2-D Gel Electrophoresis by MALDI Mass Spectrometry |
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417 | (14) |
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Identification of Posttranslational Modification by Mass Spectrometry |
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431 | (8) |
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Approaches to the O-Glycoproteome |
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439 | (20) |
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Identification of Protein Phosphorylation Sites by Mass Spectrometry |
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459 | (8) |
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Quantitative Analysis of Protein Phosphorylation Status and Protein Kinase Activity on Microassays Using Pro-Q™ Diamond Dye Technology |
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467 | (8) |
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New Challenges and Strategies for Multiple Sequence Alignment in the Proteomics Era |
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475 | (18) |
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The Clustal Series of Programs for Multiple Sequence Alignment |
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493 | (10) |
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FASTA Servers for Sequence Similarity Search |
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503 | (24) |
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Protein Sequence Analysis and Domain Identification |
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527 | (16) |
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Mammalian Genes and Evolutionary Genomics |
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543 | (12) |
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Computational Identification of Related Proteins: Blast, PSI-Blast, and Other Tools |
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555 | (16) |
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Protein Identification and Analysis Tools on the ExPASy Server |
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571 | (38) |
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Protein Sequence Databases |
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609 | (10) |
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In Silico Characterization of Proteins: InterPro and Proteome Analysis |
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619 | (10) |
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Computational Prediction of Protein-Protein Interactions |
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629 | (24) |
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The Yeast Two-Hybrid System for Detecting Interacting Proteins |
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653 | (30) |
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Antibody-Affinity Purification to Detect Interacting Proteins |
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683 | (6) |
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Biomolecular Interaction Analysis Coupled With Mass Spectrometry to Detect Interacting Proteins |
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689 | (10) |
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Assessment of Antibody--Antigen Interaction Using SELDI Technology |
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699 | (10) |
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Protein and Peptide Microarray-Based Assay Technology |
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709 | (14) |
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Production of Protein Microarrays Using Robotic Pin Printing Technologies |
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723 | (12) |
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PCR-Directed Protein In Situ Arrays |
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735 | (8) |
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Site-Specific Immobilization of Proteins in a Microarray |
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743 | (10) |
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A Guide to Protein Interaction Databases |
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753 | (48) |
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Deriving Function From Structure: Approaches and Limitations |
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801 | (30) |
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Comparative Protein Structure Modeling |
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831 | (30) |
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Classification of Protein Sequences and Structures |
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861 | (14) |
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How to Use Protein 1-D Structure Predicted by PROFphd |
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875 | (28) |
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Classification of Protein Folds |
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903 | (18) |
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921 | (18) |
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High-Throughput Crystallography for Structural Proteomics |
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939 | (16) |
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Automated High-Throughput Protein Crystallization |
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955 | (12) |
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NMR-Based Structure Determination of Proteins in Solution |
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967 | (16) |
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| Index |
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983 | |
Other versions by this Author