Walker The Proteomics Protocols Handbook

2005
ISBN: 978-1-59259-890-8
Verlag: Humana Press
Format: PDF
Kopierschutz: Wasserzeichen (»Systemvoraussetzungen)

E-Book, Englisch, 969 Seiten, eBook

Reihe: Springer Protocols Handbooks

Hands-on researchers describe in step-by-step detail 73 proven laboratory methods and bioinformatics tools essential for analysis of the proteome. These cutting-edge techniques address such important tasks as sample preparation, 2D-PAGE, gel staining, mass spectrometry, and post-translational modification. There are also readily reproducible methods for protein expression profiling, identifying protein-protein interactions, and protein chip technology, as well as a range of newly developed methodologies for determining the structure and function of a protein. The bioinformatics tools include those for analyzing 2D-GEL patterns, protein modeling, and protein identification. All laboratory-based protocols follow the successful Methods in Molecular Biology™ series format, each offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.

Written for: Biochemists, Proteomic scientists, protein researchers, molecular biologists

Zielgruppe

Research

Autoren/Hrsg.

Walker, John M.

Inhaltsverzeichnis

1;Preface;5
2;Contents;6
3;Contributors;11
4;Extraction and Solubilization of Proteins for Proteomic Studies;17
5;Preparation of Bacterial Samples for 2-D PAGE;35
6;Preparation of Yeast Samples for 2-D PAGE;43
7;Preparation of Mammalian Tissue Samples for Two- Dimensional Electrophoresis;47
8;Differential Detergent Fractionation of Eukaryotic Cells;52
9;Serum or Plasma Sample Preparation for Two- Dimensional Gel Electrophoresis;64
10;Preparation of Plant Protein Samples for 2-D PAGE;70
11;Laser-Assisted Microdissection in Proteomic Analyses;73
12;Purification of Cellular and Organelle Populations by Fluorescence- Activated Cell Sorting for Proteome Analysis;81
13;Purification of Nucleoli From Lymphoma Cells and Solubilization of Nucleolar Proteins for 2- DE Separation;93
14;Prefractionation of Complex Protein Mixture for 2-D PAGE Using Reversed- Phase Liquid Chromatography;100
15;Fractionation of Complex Proteomes by Microscale Solution Isoelectrofocusing Using ZOOM Ù IEF Fractionators to Improve Protein Profiling;109
16;Large-Format 2-D Polyacrylamide Gel Electrophoresis;130
17;Analysis of Membrane Proteins by Two-Dimensional Gels;143
18;2-D PAGE of High-Molecular-Mass Proteins;155
19;Using Ultra-Zoom Gels for High-Resolution Two- Dimensional Polyacrylamide Gel Electrophoresis;160
20;NEpHGE and pI Strip Proteomic 2-D Gel Electrophoretic Mapping of Lipid- Rich Membranes;175
21;Silver Staining of 2-D Gels;184
22;Zn2+ Reverse Staining Technique;192
23;Multiplexed Proteomics Technology for the Fluorescence Detection of Phosphorylation and Protein Expression Levels Using Pro-Q® Diamond and SYPRO® Ruby Dyes;208
24;Sensitive Quantitative Fluorescence Detection of Proteins in Gels Using SYPRO® Ruby Protein Gel Stain;216
25;Ruby Protein Gel Stain;216
26;Rapid, Sensitive Detection of Proteins in Minigels With Fluorescent Dyes;222
27;Differential In-Gel Electrophoresis in a High-Throughput Environment;230
28;Statistical Analysis of 2-D Gel Patterns;245
29;2-DE Databases on the World Wide Web;265
30;Computer Analysis of 2-D Images;273
31;Comparing 2-D Electrophoretic Gels Across Internet Databases;284
32;Sample Cleanup by Solid-Phase Extraction/Pipet-Tip Chromatography;311
33;Protein Identification by In-Gel Digestion and Mass Spectrometric Analysis;314
34;Peptide Sequences of 2-D Gel-Separated Protein Spots by Nanoelectrospray Tandem Mass Spectrometry;318
35;Identification of Proteins by MALDI-TOF MS;322
36;Sequencing of Tryptic Peptides Using Chemically Assisted Fragmentation and MALDI- PSD;328
37;The In Situ Characterization of Membrane-Immobilized 2-D PAGE-Separated Proteins Using Ink-Jet Technology;344
38;Protein Identification by Peptide Mass Fingerprinting;358
39;Analysis of the Proteomes in Human Tissues by In-Gel Isoelectric Focusing and Mass Spectrometry;369
40;Liquid Chromatography Coupled to MS for Proteome Analysis;377
41;Quantitative Analysis of Proteomes and Subproteomes by Isotope- Coded Affinity Tag and Solid- Phase Glycoprotein Capture;386
42;Amino Acid-Coded Mass Tagging for Quantitative Profiling of Differentially Expressed Proteins and Modifications in Cells;394
43;Mass-Coded Abundance Tagging for Protein Identification and Relative Abundance Determination in Proteomic Experiments;407
44;Virtual 2-D Gel Electrophoresis by MALDI Mass Spectrometry;416
45;Identification of Posttranslational Modification by Mass Spectrometry;429
46;Approaches to the O-Glycoproteome;436
47;Identification of Protein Phosphorylation Sites by Mass Spectrometry;455
48;Quantitative Analysis of Protein Phosphorylation Status and Protein Kinase Activity on Microarrays Using Pro- Q Ù Diamond Dye Technology;463
49;New Challenges and Strategies for Multiple Sequence Alignment in the Proteomics Era;470
50;The Clustal Series of Programs for Multiple Sequence Alignment;488
51;FASTA Servers for Sequence Similarity Search;498
52;Protein Sequence Analysis and Domain Identification;521
53;Mammalian Genes and Evolutionary Genomics;536
54;Computational Identification of Related Proteins;547
55;Protein Identification and Analysis Tools on the ExPASy Server;563
56;Protein Sequence Databases;600
57;Characterization of Proteins;610
58;Computational Prediction of ProteinÒProtein Interactions;619
59;The Yeast Two-Hybrid System for Detecting Interacting Proteins;643
60;Antibody-Affinity Purification to Detect Interacting Proteins;673
61;Biomolecular Interaction Analysis Coupled With Mass Spectrometry to Detect Interacting Proteins;679
62;Assessment of AntibodyÒAntigen Interaction Using SELDI Technology;689
63;Protein and Peptide Microarray-Based Assay Technology;698
64;Production of Protein Microarrays Using Robotic Pin Printing Technologies;711
65;PCR-Directed Protein In Situ Arrays;722
66;Site-Specific Immobilization of Proteins in a Microarray;730
67;A Guide to Protein Interaction Databases;739
68;Deriving Function From Structure;786
69;Comparative Protein Structure Modeling;815
70;Classification of Protein Sequences and Structures;845
71;How to Use Protein 1-D Structure Predicted by PROFphd;859
72;Classification of Protein Folds;886
73;Protein Threading;903
74;High-Throughput Crystallography for Structural Proteomics;921
75;Automated High-Throughput Protein Crystallization;936
76;NMR-Based Structure Determination of Proteins in Solution;948

Extraction and Solubilization of Proteins for Proteomic Studies Richard M. Leimgruber Preparation of Bacterial Samples for 2-D PAGE Brian Berg Vandahl, Gunna Christiansen, and Svend Birkelund Preparation of Yeast Samples for 2-D PAGE Joakim Norbeck Preparation of Mammalian Tissue Samples for Two-Dimensional Electrophoresis Frank A. Witzmann Differential Detergent Fractionation of Eukaryotic Cells Melinda L. Ramsby and Gregory S. Makowski Serum or Plasma Sample Preparation for Two-Dimensional Gel Electrophoresis Anthony G. Sullivan, Stephen Russell, Henry Brzeski, Richard I. Somiari, and Craig D. Shriver Preparation of Plant Protein Samples for 2-D PAGE David W. M. Leung Laser-Assisted Microdissection in Proteomic Analyses Darrell L. Ellsworth, Stephen Russell, Brenda Deyarmin, Anthony G. Sullivan, Henry Brzeski, Richard I. Somiari, and Craig D. Shriver Purification of Cellular and Organelle Populations by Fluorescence-Activated Cell Sorting for ProteomeAnalysis William L. Godfrey, Colette J. Rudd, Sujata Iyer, and Diether Recktenwald Purification of Nucleoli From Lymphoma Cells and Solubilization of Nucleolar Proteins for 2-DE Separation Régis Dieckmann, Yohann Couté, Denis Hochstrasser, Jean-Jacques Diaz, and Jean-Charles Sanchez Prefractionation of Complex Protein Mixture for 2-D PAGE Using Reversed-Phase Liquid Chromatography Volker Badock and Albrecht Otto Fractionation of Complex Proteomes by Microscale Solution Isoelectrofocusing Using ZOOM™ IEF Fractionators to Improve Protein Profiling Xun Zuo, Ki-Boom Lee, and David W. Speicher Large-Format 2-D Polyacrylamide Gel Electrophoresis Henry Brzeski, Stephen Russell, Anthony G. Sullivan, Richard I. Somiari, and Craig D. Shiver Analysis of Membrane Proteins by Two-Dimensional Gels MichaelFountoulakis 2-D PAGE of High-Molecular-Mass Proteins Masamichi Oh-Ishi and Tadakazu Maeda Using Ultra-Zoom Gels for High-Resolution Two-Dimensional Polyacrylamide Gel Electrophoresis Sjouke Hoving, Hans Voshol, and Jan van Oostrum NEpHGE and pI Strip Proteomic 2-D Gel Electrophoretic Mapping of Lipid-Rich Membranes Steven E. Pfeiffer, Yoshihide Yamaguchi, Cecilia B. Marta, Rashmi Bansal, and Christopher M. Taylor Silver Staining of 2-D Gels Julia Poland, Thierry Rabilloud, and Pranav Sinha Zn2+ Reverse Staining Technique Carlos Fernandez-Patron Multiplexed Proteomics Technology for the Fluorescence Detection of Glycoprotein Levels and Protein Expression Levels Using Pro-Q® Emerald and SYPRO® Ruby Dyes Birte Schulenberg and Wayne F. Patton Multiplexed Proteomics Technology for the Fluorescence Detection of Phosphorylation and Protein Expression Levels Using Pro-Q® Diamond and SYPRO® Ruby Dyes Birte Schulenberg, Terrie Goodman, Thomas H. Steinberg, and Wayne F. Patton Sensitive Quantitative Fluorescence Detection of Proteins in Gels Using SYPRO® Ruby Protein Gel Stain Birte Schulenberg, Nancy Ahnert, and Wayne F. Patton Rapid, Sensitive Detection of Proteins in Minigels With Fluorescent Dyes: Coomassie Fluor Orange, SYPRO® Orange, SYPRO Red, and SYPRO Tangerine Protein Gel Stains Thomas H. Steinberg, Courtenay R. Hart, and Wayne F. Patton Differential In-Gel Electrophoresis in a High-Throughput Environment Richard I. Somiari, Stephen Russell, Stella B. Somiari, Anthony G. Sullivan, Darrell L. Ellsworth, Henry Brzeski, and Craig D. Shriver Statistical Analysis of 2-D Gel Patterns Françoise Seillier-Moiseiwitsch 2-DE Databases on the World Wide Web Christine Hoogland, Khaled Mostaguir, and Ron D. Appel Computer Analysis of 2-D Images Patricia M. Palagi,