Describes laboratory methods and bioinformatics tools useful for analysis of the proteome. This book addresses such tasks as sample preparation, 2D-PAGE, gel staining, mass spectrometry, and post-translational modification. It also discusses reproducible methods for protein expression profiling, identifying protein-protein interactions and others.

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.

The Proteomics Handbook
Ed. John M. Walker
1. Extraction and Solubilization of Proteins for Proteomic Studies
-
Richard M.
Leimgruber
2. Preparation of Bacterial Samples for 2-D PAGE
Brian Berg Vandahl, Gunna
Christiansen and Svend Birkelund
3. Preparation of Yeast Samples for 2-D PAGE -
Joakim Norbeck
4. Preparation of Mammalian Tissue Samples for Two-Dimensional Electrophoresis -
Frank Witzmann
5. Differential Detergent Fractionation of Eukaryotic Cells
-
Melinda L. Ramsby and
Gregory S. Makowski
6. Serum or Plasma Sample Preparation for Two-Dimensional Gel Electrophoresis
-
Anthony G. Sullivan, Stephen Russell, Henry Brzeski, Richard I. Somiari and Craig D. Shriver
7. Preparation of Plant Protein Samples for 2-D PAGE
-
David W.M. Leung
8. Laser Assisted Microdissection for Sample Preparation
Darrell L. Ellsworth, Stephen Russell, Brenda Deyarmin, Anthony Sullivan, Henry Brzeski, Richard I. Somiari and Craig D. Shriver
9. Purification of Cellular
and Organelle Populations by Fluorescence-Activated Cell
Sorting for Proteome Analysis
-
William L. Godfrey,
Colette J. Rudd,
Sujata Iyer
and Diether Recktenwald
10. Purification of Nucleoli From Lymphoma Cells and Solubilization of Nucleolar Proteins for 2-DE Separations
-
Regis Dieckmann, Yohanne Coute, Denis Hochstrasser, Jean-Jacques Diaz and Jean-Charles Sanchez
11. Pre-Fractionation of Complex Protein Mixtures for 2-D PAGE Using Reversed Phase
Liquid Chromatography
Volker Badock and Albrecht Otto
12. Fractionation of Complex Proteomes by Microscale Solution Isoelectrofocusing Using ZOOM IEF Fractionators to Improve Protein Profiling
-
Xun Zuo, Ki-Beom Lee and David W. Speicher
13. Large-Format Two-Dimensional Polyacrylamide Gel Electrophoresis
-
Henry Brzeski,
Stephen Russell, Tony G. Sullivan,
Richard Somiari &

Craig Shriver
14. Analysis of Membrane Proteins by Two-Dimensional Gels
-
Michael Fountoulakis,
15. 2-D PAGE of High Molecular Mass Proteins - Masamichi Oh-Ishi
and Tadakazu
Maeda
16. Using Ultra-Zoom Gels for High Resolution Two-Dimensional Polyacrylamide Gel
Electrophoresis
Sjouke Hoving, Hans Voshol
and Jan van Oostrum
17. NEPHGE and pI Strip Proteomic Two-Dimensional Gel Electrophoretic Mapping of
Lipid-Rich Membranes
- Steven E. Pfeiffer, Yoshihide Yamaguchi, Cecilia B. Marta,
Rashmi Bansal and Christopher M. Taylor
18. Silver Staining of 2-D gels
-
Julia Poland,
Thierry Rabilloud and Pranav
Sinha
19. Zn2+ Reverse Staining Technique
Carlos Fernandez-Patron
20. 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
21. 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 Steinberg and Wayne F. Patton
22. Sensitive Quantitative Fluorescence Detection of Proteins in Gels Using
SYPRO Ruby Protein Gel Stain
-
Birte Schulenberg, Nancy Ahnert and Wayne F. Patton
23. 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
24. Difference 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
25. Statistical Analysis of 2-D Gel Patterns
-
Francoise Seillier-Moiseiwitsch
26. 2-DE Databases on the World Wide Web
- Christine Hoogland, Khaled Mostaguir
and
Ron D. Appel
27. Computer Analysis of 2-D images
Patricia M. Palagi, Daniel Walther, Gerard
Bouchet,
Sonja Voordijk
and Ron D. Appel.
28. Comparing 2D Electrophoretic Gels Across Internet Databases
- An Open Source
Application -
Peter
F. Lemkin, Gregory C. Thornwall and Jai Evans
29. Sample Cleanup by Solid Phase Extraction/Pipette Tip Chromatography
- Alastair
Aitken
30. Protein Identification by In-Gel Digestion and Mass Spectrometric Analysis
-
Michele Learmonth and Alastair Aitken
31. Peptide sequences of 2-D Gel Separated Protein Spots by Nanoelectrospray Tandem
Mass Spectrometry
- Alastair Aitken
32. Identification of Proteins by MALDI-tof
MS
- Alastair Aitken
33. Sequencing of Tryptic Peptides Using Chemically-Assisted Fragmentation MALDI-PSD -
John Flensburg and Maria Liminga
34. The In Situ Characterization of Membrane Immobilized 2-D PAGE Separated Proteins Using Ink-Jet Technology
-
Patrick
W. Cooley, Janice L. Joss, Femia G. Hopwood, Nicole L. Wilson and Andrew A. Gooley
35. Protein Identification by Peptide Mass Fingerprinting
- Alastair Aitken
36. Analysis of the Proteomes in Human Tissues by In-Gel Isoelectric Focusing and Mass Spectrometry
-
Francesco Giorgianni and Sarka Beranova-Giorgianni
37. Liquid Chromatograph Coupled to MS for Proteome
Analysis
Alastair Aitken
38. Quantitative Analysis of Proteomes and Subproteomes by Isotope Coded Affinity Tags (ICAT) and Solid-Phase Glycoprotein Capture
-
Eugene Yi, Hui Zhang, Kelly Cooke, Ruedi Aebersold and David R. Goodlett
39. Amino Acid-Coded Mass Tagging for Quantitative Profiling of Differentially Expressed Proteins
Xian Chen
40. Mass-Coded Abundance Tagging
(MCAT) for Protein Identification and Relative Abundance Determination -
Gerard Cagney and Andrew Emili
41. Virtual 2-D Gel Electrophoresis by Mass Spectrometry -
Angela Walker, Gary Rymar and Philip Andrews
42. Identification of Post-Translational Modification by Mass Spectrometry
Alastair Aitken
43. Approaches to the O-Glycoproteome - Franz-Georg Hanisch and
Stefan Muller
44. Identification of Protein Phosphorylation Sites by Mass Spectrometry
Alastair Aitken
45. Quantitative Analysis of Protein Phosphorylation Status and Protein Kinase Activity
on Microassays Using Pro-Q Diamond Dye Technology
-
Karen Martin and Wayne F. Patton
46. New Challenges and Strategies for Multiple Sequence Alignment in the Proteomics Era
-
Julie
D. Thompson and Olivier Poch
47. The Clustal Series of Programs for Multiple Sequence Alignment
Julie D. Thompson
48. FASTA
Servers for Sequence Similarity Search
-
Biju Issac and Gajendra P.S.
Raghava
49.
Protein Sequence Analysis and Domain Identification
-
Chris P. Ponting and Ewan
Birney
50. Mammalian Genes and Evolutionary Genomics
-
Leo Goodstadt and Chris Ponting
51. Computational Identification of Related Proteins: BLAST and PSI-BLAST and Other Tools
Qunfeng Dong and Volker Brendel
52. Protein Identification and Analysis Tools on the
ExPASy Server
- Elizabeth Gasteiger, Christine Hoogland, Alexandre Gattiker, Severine Duvaud, Mark Wilkins,
Ron D. Appel and Amos
Bairoch
53. Protein Sequence Databases
-
Michele Magrane, Maria Jesus Martin, Claire
O'Donovan and Rolf Apweiler
54. In Silico Characterization of Proteins
InterPro and Proteome Analysis
-
Nicola
Jane Mulder,
Manuela Pruess and Rolf Apweiler
55. Computational Prediction of P0rotein-Protein Interactions
-
Anton J. Enright, Lucy
Skrabanek and Gary D. Bader
56. The Yeast Two-Hybrid System for Detecting Interacting Proteins
Ilya G. Serebriiskii, Erica A. Golemis and Peter Uetz
57. Antibody-Affinity Purification to Detect Interacting Proteins
-
Sonia Navarro and
Lucio Comai
58. Biomolecular Interaction Analysis Coupled with Mass Spectrometry to Detect Interacting Proteins
-
Setsuko Hashimoto, Toshiaki Isobe and Tohru Natsume
59. Assessment of Antibody-Antigen Interaction Using SELDI
Technology
-
Li-Shen Hsieh,
Ramy Moharram , Emilio Caputo and Brian M. Martin
60. Protein and Peptide Microarray-Based Assay Technology
-
Scott T. Clarke
61. Production of Protein Microarrays Using Robotic Pin Printing Technologies
Ye
Fang, Ann M. Ferrie and Fang Lai
62. PCR-Directed Protein In Situ Arrays
-
Joe Boutell and Mingyue He
63. Site-Specific Immobilization of Proteins in a Microarray
-
Yee Peng R. Lue,
Su-Yin D. Yeo,
Lay Pheng Tan, Grace Y.J. Chen and Shao Q. Yao
64. A Guide to Protein Interaction Databases -
Tiffany B. Fischer,
Melissa Paczkowski,
Michael F. Zettel and Jerry Tsai
65. Deriving Function From Structure:
Approaches and Limitations
Annabel E. Todd
66. Comparative Protein Structure Modelling
-
M.S. Madhusudhan, Marc A. Marti Renom, Narayanan Eswar, Bino John, Ursula Pieper, Rachel Karchin, Min-Yi Shen and Andrej Sali
67. Classification of Protein Sequences and Structures -
Shalom Rackovsky
68. How to Use Protein 1D Structure Predicted by PROFphd -
Burkhard
Rost
69. Classification of Proteins Folds
-
Rob Russell
70. Protein Threading
-
Andrew E. Torda
71. High Throughput Crystallography for Structural Proteomics
Jeff Yon,
Mladen Vinkovic and Harren Jhoti
72. Automated High-Throughput Protein Crystallization
-
Arezou Azarani
73. NMR-Based
Structure Determination of Proteins in Solution -
Andrzej Ejchart and
Igor Zhukov