The proteomics protocols handbook [electronic resource] / edited by John M. Walker.

Contributor(s): Walker, John M, 1948-
Material type: TextTextPublisher: Totowa, N.J. : Humana Press, ©2005Description: 1 online resource (xviii, 988 pages) : illustrationsContent type: text Media type: computer Carrier type: online resourceISBN: 1592598900; 9781592598908; 1423714946; 9781423714941; 1588295931; 9781588295934Subject(s): Proteomics -- Handbooks, manuals, etc | Protéomique | SCIENCE -- Life Sciences -- Biochemistry | Proteomics -- methods | Proteomics | Biomédecine | Sciences de la vie | Proteomics | Eiwitten | Eiwitsynthese | Transcriptiefactoren | Wetenschappelijke technieken | Proteomanalyse | Proteins | Genetics | Science -- Chemistry -- Organic | Science -- Life Sciences -- Genetics & Genomics | Proteomics -- methods | Proteomics -- methodsGenre/Form: Electronic books. | Electronic books. | Handbooks and manuals. | Aufsatzsammlung. Additional physical formats: No titleDDC classification: 572/.6 LOC classification: QP551 | .P75675 2005Other classification: Q51-62 | 35.75 | 35.71 Online resources: Click here to access online
Contents:
In: OhioLINK electronic book center In: SpringerLinkSummary: Proteomics methodology has revolutionized the way that proteins are studied and opened new channels to understanding both cell functions and the cellular changes involved in disease states. In The Proteomics Protocols Handbook, hands-on researchers describe in step-by-step detail a wide range of proven laboratory methods and bioinformatics tools essential for analysis of the proteome. These cutting-edge techniques (73 in all) address such important tasks as sample preparation, 2D-PAGE, gel staining, mass spectrometry, and posttranslational 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, including novel mass spectrometry and LC-MS techniques, protein array technology, and a variety of structural and functional proteomics techniques needed to determine of the function of newly discovered protein sequences. The use of X-ray crystallography and NMR to determine protein structure is also described. 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. Timely and highly practical, The Proteomics Protocols Handbook offers molecular biologists, protein chemists, clinical and medicinal chemists, biochemists, and microbiologists a comprehensive collection of today's best tools for understanding not only the function of individual proteins in the cell, but also for identifying new therapeutic targets.
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Proteomics methodology has revolutionized the way that proteins are studied and opened new channels to understanding both cell functions and the cellular changes involved in disease states. In The Proteomics Protocols Handbook, hands-on researchers describe in step-by-step detail a wide range of proven laboratory methods and bioinformatics tools essential for analysis of the proteome. These cutting-edge techniques (73 in all) address such important tasks as sample preparation, 2D-PAGE, gel staining, mass spectrometry, and posttranslational 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, including novel mass spectrometry and LC-MS techniques, protein array technology, and a variety of structural and functional proteomics techniques needed to determine of the function of newly discovered protein sequences. The use of X-ray crystallography and NMR to determine protein structure is also described. 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. Timely and highly practical, The Proteomics Protocols Handbook offers molecular biologists, protein chemists, clinical and medicinal chemists, biochemists, and microbiologists a comprehensive collection of today's best tools for understanding not only the function of individual proteins in the cell, but also for identifying new therapeutic targets.

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Machine derived contents note: Contents -- Preface vii -- Contributors xiii -- 1 Extraction and Solubilization of Proteins for Proteomic Studies -- Richard M. Leimgruber xx -- 2 Preparation of Bacterial Samples for 2-D PAGE -- Brian Berg Vandahl, Gunna Christiansen, and Svend Birkelund xx -- 3 Preparation of Yeast Samples for 2-D PAGE -- Joakim Norbeck xx -- 4 Preparation of Mammalian Tissue Samples for 2-D Electrophoresis -- Frank Witzmann xx -- 5 Differential Detergent Fractionation of Eukaryotic Cells -- Gregory S. Makowski xx -- 6 Serum or Plasma Sample Preparation for 2-D Gel Electrophoresis -- Anthony G. Sullivan, Stephen Russell, Henry Brzeski, Richard I. Somiari, -- and Craig D. Shriver xx -- 7 Preparation of Plant Protein Samples for 2-D PAGE -- David W. M. Leung xx -- 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 xx -- 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 xx -- 10 Purification of Nucleoli From Lymphoma Cells and Solubilization -- of Nucleolar Proteins for 2-DE Separations -- Regis Dieckmann, Yohanne CoutÄ, Denis Hochstrasser, -- Jean-Jacques Diaz, and Jean-Charles Sanchez xx -- 11 Prefractionation of Complex Protein Mixtures for 2-D PAGE -- Using Reversed-Phase Liquid Chromatography -- Volker Badock and Albrecht Otto xx -- 12 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 xx -- 13 Large-Format 2-D Polyacrylamide Gel Electrophoresis -- Henry Brzeski, Stephen Russell, Tony G. Sullivan, Richard Somiari, -- and Craig Shiver xx -- 14 Analysis of Membrane Proteins by 2-D Gels -- Michael Fountoulakis xx -- 15 2-D PAGE of High-Molecular-Mass Proteins -- Masamichi Oh-Ishi and Tadakazu Maeda xx -- 16 Using Ultra-Zoom Gels for High-Resolution 2-D Polyacrylamide -- Gel Electrophoresis -- Sjouke Hoving, Hans Voshol, and Jan van Oostrum xx -- 17 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 xx -- 18 Silver Staining of 2-D Gels -- Julia Poland, Thierry Rabilloud, and Pranav Sinha xx -- 19 Zn2+ Reverse Staining Technique -- Carlos Fernandez-Patron xx -- 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 xx -- 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 xx -- 22 Sensitive Quantitative Fluorescence Detection of Proteins in Gels -- Using SYPRO Ruby Protein Gel Stain -- Birte Schulenberg, Nancy Ahnert, and Wayne F. Patton xx -- 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 xx -- 24 Difference Gel Electrophoresis in a High-Throughput Environment -- Stephen Russell, Stella B. Somiari, Anthony G. Sullivan, -- Darrell L. Ellsworth, Henry Brzeski, and Craig D. Shriver xx -- 25 Statistical Analysis of 2-D Gel Patterns -- Francoise Seillier-Moiseiwitsch xx -- 26 2-DE Databases on the World Wide Web -- Christine Hoogland, Khaled Mostaguir, and Ron D. Appel xx -- 27 Computer Analysis of 2-D Images -- Patricia M. Palagi, Daniel Walther, GÄrard Bouchet, Sonja Voordijk, -- and Ron D. Appel xx -- 28 Comparing 2-D Electrophoretic Gels Across Internet Databases: -- An Open Source Application -- Peter F. Lemkin, Gregory C. Thornwall, and Jai Evans xx -- 29 Sample Cleanup by Solid-Phase Extraction/Pipet Tip Chromatography -- Alastair Aitken xx -- 30 Protein Identification by In-Gel Digestion and Mass Spectrometric Analysis -- Michele Learmonth and Alastair Aitken xx -- 31 Peptide Sequences of 2-D Gel Separated Protein Spots -- by Nanoelectrospray Tandem Mass Spectrometry -- Alastair Aitken xx -- 32 Identification of Proteins by MALDI-tof MS -- Alastair Aitken xx -- 33 Sequencing of Tryptic Peptides Using Chemically-Assisted Fragmentation -- Maldi-Psd -- John Flensburg and Maria Liminga xx -- 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 xx -- 35 Protein Identification by Peptide Mass Fingerprinting -- Alastair Aitken xx -- 36 Analysis of the Proteomes in Human Tissues by In-Gel Isoelectric Focusing -- and Mass Spectrometry -- Francesco Giorgianni and Sarka Beranova-Giorgianni xx -- 37 Liquid Chromatograph Coupled to MS for Proteome Analysis -- Alastair Aitken xx -- 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 xx -- 39 Amino Acid-Coded Mass Tagging for Quantitative Profiling -- of Differentially Expressed Proteins -- Xian Chen xx -- 40 Mass-Coded Abundance Tagging (MCAT) for Protein Identification -- and Relative Abundance Determination -- Gerard Cagney and Andrew Emili xx -- 41 Virtual 2-D Gel Electrophoresis by Mass Spectrometry -- Angela Walker, Gary Rymar, and Philip Andrews xx -- 42 Identification of Posttranslational Modification by Mass Spectrometry -- Alastair Aitken xx -- 43 Approaches to the O-Glycoproteome -- Franz-Georg Hanisch and Stefan M#x83;ller xx -- 44 Identification of Protein Phosphorylation Sites by Mass Spectrometry -- Alastair Aitken vv -- 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 xx -- 46 New Challenges and Strategies for Multiple Sequence Alignment -- in the Proteomics Era -- Julie D. Thompson and Olivier Poch xx -- 47 The Clustal Series of Programs for Multiple Sequence Alignment -- Julie D. Thompson xx -- 48 FASTA Servers for Sequence Similarity Search -- Biju Issac and Gajendra P. S. Raghava xx -- 49 Protein Sequence Analysis and Domain Identification -- Chris P. Ponting and Ewan Birney xx -- 50 Mammalian Genes and Evolutionary Genomics -- Leo Goodstadt and Chris Ponting xx -- 51 Computational Identification of Related Proteins: -- BLAST and PSI-BLAST and Other Tools -- Qunfeng Dong and Volker Brendel xx -- 52 Protein Identification and Analysis Tools on the ExPASy Server -- Elizabeth Gasteiger, Christine Hoogland, Alexandre Gattiker, -- SÄverine Duvaud, Mark Wilkins, Ron D. Appel xx -- 53 Protein Sequence Databases -- Michele Magrane, Maria Jesus Martin, Claire OÔDonovan, -- and Rolf Apweiler xx -- 54 In Silico Characterization of Proteins: InterPro and Proteome Analysis -- Nicola Jane Mulder, Manuela Pruess, and Rolf Apweiler xx -- 55 Computational Prediction of Protein/Protein Interactions -- Anton J. Enright, Lucy Skrabanek, and Gary D. Bader xx -- 56 The Yeast Two-Hybrid System for Detecting Interacting Proteins -- Ilya G. Serebriiskii, Erica A.

Golemis, and Peter Uetz xx -- 57 Antibody-Affinity Purification to Detect Interacting Proteins -- Sonia Navarro and Lucio Comai xx -- 58 Biomolecular Interaction Analysis Coupled With Mass Spectrometry -- to Detect Interacting Proteins -- Setsuko Hashimoto, Toshiaki Isobe, and Tohru Natsume xx -- 59 Assessment of Antibody-Antigen Interaction Using SELDI Technology -- Li-Shen Hsieh, Ramy Moharram, Emilio Caputo, and Brian M. Martin xx -- 60 Protein and Peptide Microarray-Based Assay Technology -- Scott T. Clarke xx -- 61 Production of Protein Microarrays Using Robotic Pin Printing Technologies -- Ye Fang, Ann M. Ferrie, and Fang Lai xx -- 62 PCR-Directed Protein In Situ Arrays -- Joe Boutell and Minyue He xx -- 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 xx -- 64 A Guide to Protein Interaction Databases -- Tiffany B. Fischer, Melissa Paczkowski, Michael F. Zettel, and Jerry Tsai xx -- 65 Deriving Function from Structure: Approaches and Limitations -- Annabel E. Todd xx -- 66 Comparative Protein Structure Modeling -- M. S. Madhusudhan, Marc A. Marti Renom, Narayanan Eswar, Bino John, -- Ursula Pieper, Rachel Karchin, Min-Yi Shen, and Andrej Sali xx -- 67 Classification of Protein Sequences and Structures -- Shalom Rackovsky xx -- 68 How to Use Protein 1D Structure Predicted by PROFphd -- Burkhard Rost xx -- 69 Classification of Proteins Folds -- Rob Russell xx -- 70 Protein Threading -- Andrew E. Torda xx -- 71 High-Throughput Crystallography for Structural Proteomics -- Jeff Yon, Mladen Vinkovic, and Harren Jhoti xx -- 72 Automated High-Throughput Protein Crystallization -- Arezou Azarani xx -- 73 NMR-Based Structure Determination of Proteins in Solution -- Andrzej Ejchart and Igor Zhukov xx -- Index xxx.

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