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 Proteome Analysis 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 Regis Dieckmann, Yohann Coute, 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(t) 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 Michael Fountoulakis 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(R) Emerald and SYPRO(R) Ruby Dyes Birte Schulenberg and Wayne F. Patton Multiplexed Proteomics Technology for the Fluorescence Detection of Phosphorylation and Protein Expression Levels Using Pro-Q(R) Diamond and SYPRO(R) Ruby Dyes Birte Schulenberg, Terrie Goodman, Thomas H. Steinberg, and Wayne F. Patton Sensitive Quantitative Fluorescence Detection of Proteins in Gels Using SYPRO(R) 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(R) 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 Francoise 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, Daniel Walther, Gerard Bouchet, Sonja Voordijk, and Ron D. Appel Comparing 2-D Electrophoretic Gels Across Internet Databases: An Open Source Application Peter F. Lemkin, Gregory C. Thornwall, and Jai Evans Sample Cleanup by Solid-Phase Extraction/Pipet-Tip Chromatography Alastair Aitken Protein Identification by In-Gel Digestion and Mass Spectrometric Analysis Michele Learmonth and Alastair Aitken Peptide Sequences of 2-D Gel-Separated Protein Spots by Nanoelectrospray Tandem Mass Spectrometry Alastair Aitken Identification of Proteins by MALDI-TOF MS Alastair Aitken Sequencing of Tryptic Peptides Using Chemically Assisted Fragmentation and MALDI-PSD John Flensburg and Maria Liminga 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, Nichole L. Wilson, and Andrew A. Gooley Protein Identification by Peptide Mass Fingerprinting Alastair Aitken Analysis of the Proteomes in Human Tissues by In-Gel Isoelectric Focusing and Mass Spectrometry Francesco Giorgianni and Sarka Beranova-Giorgianni Liquid Chromatography Coupled to MS for Proteome Analysis Alastair Aitken Quantitative Analysis of Proteomes and Subproteomes by Isotope-Coded Affinity Tags and Solid-Phase Glycoprotein Capture Eugene Yi, Hui Zhang, Kelly Cooke, Ruedi Aebersold, and David R. Goodlett Amino Acid-Coded Mass Tagging for Quantitative Profiling of Differentially Expressed Proteins and Modifications in Cells Xian Chen Mass-Coded Abundance Tagging for Protein Identification and Relative Abundance Determination in Proteomic Experiments Gerard Cagney and Andrew Emili Virtual 2-D Gel Electrophoresis by MALDI Mass Spectrometry Angela K. Walker, Gary Rymar, and Philip C. Andrews Identification of Posttranslational Modification by Mass Spectrometry Alastair Aitken Approaches to the O-Glycoproteome Franz-Georg Hanisch and Stefan Muller Identification of Protein Phosphorylation Sites by Mass Spectrometry Alastair Aitken Quantitative Analysis of Protein Phosphorylation Status and Protein Kinase Activity on Microassays Using Pro-Q(t) Diamond Dye Technology Karen Martin and Wayne F. Patton New Challenges and Strategies for Multiple Sequence Alignment in the Proteomics Era Julie D. Thompson and Olivier Poch The Clustal Series of Programs for Multiple Sequence Alignment Julie D. Thompson FASTA Servers for Sequence Similarity Search Biju Issac and Gajendra P. S. Raghava Protein Sequence Analysis and Domain Identification Chris P. Ponting and Ewan Birney Mammalian Genes and Evolutionary Genomics Leo Goodstadt and Chris P. Ponting Computational Identification of Related Proteins: BLAST, PSI-BLAST, and Other Tools Qunfeng Dong and Volker Brendel Protein Identification and Analysis Tools on the ExPASy Server Elisabeth Gasteiger, Christine Hoogland, Alexandre Gattiker, Severine Duvaud, Marc R. Wilkins, Ron D. Appel, and Amos Bairoch Protein Sequence Databases Michele Magrane, Maria Jesus Martin, Claire O'Donovan, and Rolf Apweiler In Silico Characterization of Proteins: InterPro and Proteome Analysis Nicola Jane Mulder, Manuela Pruess, and Rolf Apweiler Computational Prediction of Protein-Protein Interactions Anton J. Enright, Lucy Skrabanek, and Gary D. Bader The Yeast Two-Hybrid System for Detecting Interacting Proteins Ilya G. Serebriiskii, Erica A. Golemis, and Peter Uetz Antibody-Affinity Purification to Detect Interacting Proteins Sonia Navarro and Lucio Comai Biomolecular Interaction Analysis Coupled With Mass Spectrometry to Detect Interacting Proteins Setsuko Hashimoto, Toshiaki Isobe, and Tohru Natsume Assessment of Antibody-Antigen Interaction Using SELDI Technology Li-Shan Hsieh, Ramy Moharram, Emilia Caputo, and Brian M. Martin Protein and Peptide Microarray-Based Assay Technology Scott T. Clarke Production of Protein Microarrays Using Robotic Pin Printing Technologies Ye Fang, Ann M. Ferrie, and Fang Lai PCR-Directed Protein In Situ Arrays Joe Boutell and Mingyue He 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 A Guide to Protein Interaction Databases Tiffany B. Fischer, Melissa Paczkowski, Michael F. Zettel, and Jerry Tsai Deriving Function From Structure: Approaches and Limitations Annabel E. Todd 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 Classification of Protein Sequences and Structures S. Rackovsky How to Use Protein 1-D Structure Predicted by PROFphd Burkhard Rost Classification of Protein Folds Robert B. Russell Protein Threading Andrew E. Torda High-Throughput Crystallography for Structural Proteomics Jeff Yon, Mladen Vinkovic, and Harren Jhoti Automated High-Throughput Protein Crystallization Arezou Azarani NMR-Based Structure Determination of Proteins in Solution Andrzej Ejchart and Igor Zhukov Index
