The Proteomics Protocols Handbook (eBook)

John M. Walker (Herausgeber)

eBook Download: PDF

2007 | 2005
XVIII, 988 Seiten
Humana Press (Verlag)
978-1-59259-890-8 (ISBN)

Infos

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

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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(TM) 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.   

Inhalt

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

Produkt-Details

• Erscheint lt. Verlag: 9.10.2007
• Reihe/Serie: Springer Protocols Handbooks
• Reihe/Serie: Springer Protocols Handbooks
• Zusatzinfo: XVIII, 988 p.
• Verlagsort: Totowa
• Sprache: englisch
• Themenwelt: Studium ► 1. Studienabschnitt (Vorklinik) ► Biochemie / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Biologie ► Biochemie
• Themenwelt: Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie
• Themenwelt: Technik
• Schlagworte: Biology • Membrane Proteins • Molecular Biology • phosphorylation • Protein • Proteomics • Translation
• ISBN-10: 1-59259-890-0 / 1592598900
• ISBN-13: 978-1-59259-890-8 / 9781592598908