The Proteomics Protocols Handbook

by Walker, John M.

• ISBN13: 9781588295934
• ISBN10: 1588295931
• Format: Paperback
• Copyright: 2005-04-01
• Publisher: Humana Pr Inc

Summary

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.

Table of Contents

Preface	vii
Contributors	xiii
Extraction and Solubilization of Proteins for Proteomic Studies	1	(18)
Richard M. Leimgruber
Preparation of Bacterial Samples for 2-D Page	19	(8)
Brian Berg Vandahl
Gunna Christiansen
Svend Birkelund
Preparation of Yeast Samples for 2-D Page	27	(4)
Joakim Norbeck
Preparation of Mammalian Tissue Samples for Two-Dimensional Electrophoresis	31	(6)
Frank A. Witzmann
Differential Detergent Fractionation of Eukaryotic Cells	37	(12)
Melinda L. Ramsby
Gregory S. Makowski
Serum or Plasma Sample Preparation for Two-Dimensional Gel Electrophoresis	49	(6)
Anthony G. Sullivan
Stephen Russell
Henry Brzeski
Richard I. Somiari
Craig D. Shriver
Preparation of Plant Protein Samples for 2-D Page	55	(4)
David W. M. Leung
Laser-Assisted Microdissection in Proteomic Analyses	59	(8)
Darrell L. Ellsworth
Stephen Russell
Brenda Deyarmin
Anthony G. Sullivan
Henry Brzeski
Richard I. Somiari
Craig D. Shriver
Purification of Cellular and Organelle Populations by Fluorescence-Activated Cell Sorting for Proteome Analysis	67	(12)
William L. Godfrey
Colette J. Rudd
Sujata Iyer
Diether Recktenwald
Purification of Nucleoli From Lymphoma Cells and Solubilization of Nucleolar Proteins for 2-DE Separation	79	(8)
Regis Dieckmann
Yohann Coute
Denis Hochstrasser
Jean-Jacques Diaz
Jean-Charles Sanchez
Prefractionation of Complex Protein Mixture for 2-D Page Using Reversed-Phase Liquid Chromatography	87	(10)
Volker Badock
Albrecht Otto
Fractionation of Complex Proteomes by Microscale Solution Isoelectrofocusing Using Zoom™ IEF Fractionators to Improve Protein Profiling	97	(22)
Xun Zuo
Ki-Boom Lee
David W. Speicher
Large-Format 2-D Polyacrylamide Gel Electrophoresis	119	(14)
Henry Brzeski
Stephen Russell
Anthony G. Sullivan
Richard I. Somiari
Craig D. Shiver
Analysis of Membrane Proteins by Two-Dimensional Gels	133	(12)
Michael Fountoulakis
2-D Page of High-Molecular-Mass Proteins	145	(6)
Masamichi Oh-Ishi
Tadakazu Maeda
Using Ultra-Zoom Gels for High-Resolution Two-Dimensional Polyacrylamide Gel Electrophoresis	151	(16)
Sjouke Hoving
Hans Voshol
Jan van Oostrum
NEpHGE and pl Strip Proteomic 2-D Gel Electrophoretic Mapping of Lipid-Rich Membranes	167	(10)
Steven E. Pfeiffer
Yoshihide Yamaguchi
Cecilia B. Marta
Rashmi Bansal
Christopher M. Taylor
Silver Staining of 2-D Gels	177	(8)
Julia Poland
Thierry Rabilloud
Pranav Sinha
Zn2+ Reverse Staining Technique	185	(8)
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	193	(8)
Birte Schulenberg
Wayne F. Patton
Multiplexed Proteomics Technology for the Fluorescence Detection of Phosphorylation and Protein Expression Levels Using Pro-Q® Diamond and Sypro® Ruby Dyes	201	(8)
Birte Schulenberg
Terrie Goodman
Thomas H. Steinberg
Wayne F. Patton
Sensitive Quantitative Fluorescence Detection of Proteins in Gels Using Sypro® Ruby Protein Gel Stain	209	(6)
Birte Schulenberg
Nancy Ahnert
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	215	(8)
Thomas H. Steinberg
Courtenay R. Hart
Wayne F. Patton
Differential In-Gel Electrophoresis in a High-Throughput Environment	223	(16)
Richard I. Somiari
Stephen Russell
Stella B. Somiari
Anthony G. Sullivan
Darrell L. Ellsworth
Henry Brzeski
Craig D. Shriver
Statistical Analysis of 2-D Gel Patterns	239	(20)
Francoise Seillier-Moiseiwitsch
2-DE Databases on the World Wide Web	259	(8)
Christine Hoogland
Khaled Mostaguir
Ron D. Appel
Computer Analysis of 2-D Images	267	(12)
Patricia M. Palagi
Daniel Walther
Gerard Bouchet
Sonja Voordijk
Ron D. Appel
Comparing 2-D Electrophoretic Gels Across Internet Databases: An Open Source Application	279	(28)
Peter F. Lemkin
Gregory C. Thornwall
Jai Evans
Sample Cleanup by Solid-Phase Extraction/Pipet-Tip Chromatography	307	(4)
Alastair Aitken
Protein Identification by In-Gel Digestion and Mass Spectrometric Analysis	311	(4)
Michele Learmonth
Alastair Aitken
Peptide Sequences of 2-D Gel-Separated Protein Spots by Nanoelectrospray Tandem Mass Spectrometry	315	(4)
Alastair Aitken
Identification of Proteins by MALDI-TOF MS	319	(6)
Alastair Aitken
Sequencing of Tryptic Peptides Using Chemically Assisted Fragmentation and MALDI-PSD	325	(16)
John Flensburg
Maria Liminga
The In Situ Characterization of Membrane-Immobilized 2-D Page-Separated Proteins Using Ink-Jet Technology	341	(14)
Patrick W. Cooley
Janice L. Joss
Femia G. Hopwood
Nichole L. Wilson
Andrew A. Gooley
Protein Identification by Peptide Mass Fingerprinting	355	(12)
Alastair Aitken
Analysis of the Proteomes in Human Tissues by In-Gel Isoelectric Focusing and Mass Spectrometry	367	(8)
Francesco Giorgianni
Sarka Beranova-Giorgianni
Liquid Chromatography Coupled to MS for Proteome Analysis	375	(10)
Alastair Aitken
Quantitative Analysis of Proteomes and Subproteomes by Isotope-Coded Affinity Tags and Solid-Phase Glycoprotein Capture	385	(8)
Eugene Yi
Hui Zhang
Kelly Cooke
Ruedi Aebersold
David R. Goodlett
Amino Acid-Coded Mass Tagging for Quantitative Profiling of Differentially Expressed Proteins and Modifications in Cells	393	(14)
Xian Chen
Mass-Coded Abundance Tagging for Protein Identification and Relative Abundance Determination in Proteomic Experiments	407	(10)
Gerard Cagney
Andrew Emili
Virtual 2-D Gel Electrophoresis by MALDI Mass Spectrometry	417	(14)
Angela K. Walker
Gary Rymar
Philip C. Andrews
Identification of Posttranslational Modification by Mass Spectrometry	431	(8)
Alastair Aitken
Approaches to the O-Glycoproteome	439	(20)
Franz-Georg Hanisch
Stefan Muller
Identification of Protein Phosphorylation Sites by Mass Spectrometry	459	(8)
Alastair Aitken
Quantitative Analysis of Protein Phosphorylation Status and Protein Kinase Activity on Microassays Using Pro-Q™ Diamond Dye Technology	467	(8)
Karen Martin
Wayne F. Patton
New Challenges and Strategies for Multiple Sequence Alignment in the Proteomics Era	475	(18)
Julie D. Thompson
Olivier Poch
The Clustal Series of Programs for Multiple Sequence Alignment	493	(10)
Julie D. Thompson
FASTA Servers for Sequence Similarity Search	503	(24)
Biju Issac
Gajendra P. S. Raghava
Protein Sequence Analysis and Domain Identification	527	(16)
Chris P. Ponting
Ewan Birney
Mammalian Genes and Evolutionary Genomics	543	(12)
Leo Goodstadt
Chris P. Ponting
Computational Identification of Related Proteins: Blast, PSI-Blast, and Other Tools	555	(16)
Qunfeng Dong
Volker Brendel
Protein Identification and Analysis Tools on the ExPASy Server	571	(38)
Elisabeth Gasteiger
Christine Hoogland
Alexandre Gattiker
Severine Duvaud
Marc R. Wilkins
Ron D. Appel
Amos Bairoch
Protein Sequence Databases	609	(10)
Michele Magrane
Maria Jesus Martin
Claire O'Donovan
Rolf Apweiler
In Silico Characterization of Proteins: InterPro and Proteome Analysis	619	(10)
Nicola Jane Mulder
Manuela Pruess
Rolf Apweiler
Computational Prediction of Protein-Protein Interactions	629	(24)
Anton J. Enright
Lucy Skrabanek
Gary D. Bader
The Yeast Two-Hybrid System for Detecting Interacting Proteins	653	(30)
Ilya G. Serebriiskii
Erica A. Golemis
Peter Uetz
Antibody-Affinity Purification to Detect Interacting Proteins	683	(6)
Sonia Navarro
Lucio Comai
Biomolecular Interaction Analysis Coupled With Mass Spectrometry to Detect Interacting Proteins	689	(10)
Setsuko Hashimoto
Toshiaki Isobe
Tohru Natsume
Assessment of Antibody--Antigen Interaction Using SELDI Technology	699	(10)
Li-Shan Hsieh
Ramy Moharram
Emilia Caputo
Brian M. Martin
Protein and Peptide Microarray-Based Assay Technology	709	(14)
Scott T. Clarke
Production of Protein Microarrays Using Robotic Pin Printing Technologies	723	(12)
Ye Fang
Ann M. Ferrie
Fang Lai
PCR-Directed Protein In Situ Arrays	735	(8)
Joe Boutell
Mingyue He
Site-Specific Immobilization of Proteins in a Microarray	743	(10)
Yee-Peng R. Lue
Su-Yin D. Yeo
Lay-Pheng Tan
Grace Y. J. Chen
Shao Q. Yao
A Guide to Protein Interaction Databases	753	(48)
Tiffany B. Fischer
Melissa Paczkowski
Michael F. Zettel
Jerry Tsai
Deriving Function From Structure: Approaches and Limitations	801	(30)
Annabel E. Todd
Comparative Protein Structure Modeling	831	(30)
M. S. Madhusudhan
Marc A. Marti-Renom
Narayanan Eswar
Bino John
Ursula Pieper
Rachel Karchin
Min-Yi Shen
Andrej Sali
Classification of Protein Sequences and Structures	861	(14)
S. Rackovsky
How to Use Protein 1-D Structure Predicted by PROFphd	875	(28)
Burkhard Rost
Classification of Protein Folds	903	(18)
Robert B. Russell
Protein Threading	921	(18)
Andrew E. Torda
High-Throughput Crystallography for Structural Proteomics	939	(16)
Jeff Yon
Mladen Vinkovic
Harren Jhoti
Automated High-Throughput Protein Crystallization	955	(12)
Arezou Azarani
NMR-Based Structure Determination of Proteins in Solution	967	(16)
Andrzej Ejchart
Igor Zhukov
Index	983