A step-by-step tour through the complete process of doing proteomics. With easy-to-follow instructions, complete with many helpful hints and explanations, leading investigators and pioneers in the field show how to make protein extracts, reproducibly run them on 2-D gels, detect them, analyze the data, and precisely identify each protein. The book covers the latest methods of using carrier ampholytes in the 1st dimension, casting and running immobilized pH gradient 2-D gels, MALDI-TOF-based peptide mapping, automated tandem mass spectrometry, and nanoelectrospray ionization technology. For the 2nd dimension, there are methods for running flatbed or vertical gels and for protein detection using autoradiography, and Coomassie, silver, and reversible metal-chelate stains. 2-D Proteome Analysis Protocols is the most complete guide for using proteomics to answer biological questions.

2-D Protein Gel Electrophoresis: An Overview, Jenny Fichmann and Reiner Westermeier. Solubilization of Proteins in 2-D Electrophoresis: An Outline, Thierry Rabilloud. Preparation of Escherichia coli Samples for 2-D Gel Analysis, Ruth A. VanBogelen and Frederick C. Neidhardt. Preparing 2-D Protein Extracts from Yeast, David M. Schieltz. 2-D Protein Extracts from Drosophila melanogaster, Christer Ericsson. Preparing 2-D Protein Extracts from Caenorhabditis elegans, Robert Zwilling. Eukaryotic Cell Labeling and Preparation for 2-D, Nick Bizios. Differential Detergent Fractionation of Eukaryotic Cells: Analysis by Two-Dimensional Gel Electrophoresis, Melinda L. Ramsby and Gregory S. Makowski. Fractionated Extraction of Total Tissue Proteins from Mouse and Human for 2-D Electrophoresis, Joachim Klose. Preparation and Solubilization of Body Fluids for 2-D, Jean Charles Sanchez and Denis F. Hochstrasser. 2-D Electrophoresis of Plant Proteins, Akira Tsugita and Masaharu Kamo. Quantifying Protein in 2-D PAGE Solubilization Buffers, Louis S. Ramagli. Measuring the Radioactivity of 2-D Protein Extracts, Andrew J. Link and Nick Bizios. Advantages of Carrier Ampholyte IEF, Mary F. Lopez. 2-D Electrophoresis Using Carrier Ampholytes in the First Dimension (IEF), Mary F. Lopez. Nonequilibrium pH Gel Electrophoresis (NEPHGE), Mary F. Lopez. High Resolution, 2-D Protein Electrophoresis Using Nondedicated Equipment, Marion Sarmiento. Large-Gel 2-D Electrophoresis, Joachim Klose. Advantages of Immobilized pH Gradients, Jenny Fichmann. Casting Immobilized pH Gradients (IPGs), Elisabetta Gianazza. Analytical IPG-Dalt, Angelika Görg and Walter Weiss. IPG-Dalt of Very Alkaline Proteins, Angelika Görg. Running Preparative Carrier Ampholyte and Immobilized pH Gradient IEF Gels for 2-D, Neil M. Matsui, Diana M. Smith-Beckerman, Jenny Fichmann, and Lois B. Epstein. In-Gel Sample Rehydration of Immobilized pH Gradient, Jean-Charles Sanchez, Denis Hochstrasser, and Thierry Rabilloud.High-Resolution, IPG-Based, Mini Two-Dimensional Gel Electrophoresis, Jean-Charles Sanchez and Denis F. Hochstrasser. Horizontal SDS-PAGE for IPG-Dalt, Angelika Görg and Walter Weiss. Casting and Running Vertical Slab-Gel Electrophoresis for 2D-PAGE, Bradley J. Walsh and Benjamin R. Herbert. Nonreducing 2-D Polyacrylamide Gel Electrophoresis, Hong Ji and Richard J. Simpson. 2-D Diagonal Gel Electrophoresis, Joan Goverman. 2-D Phosphopeptide Mapping, Hikaru Nagahara, Robert R. Latek, Sergei A. Ezhevsky, and Steven F. Dowdy. Internal Standards for 2-D, Andrew J. Link. Autoradiography of 2-D Gels, Andrew J. Link. Double-Label Analysis, Kelvin H. Lee and Michael G. Harrington. Silver Staining of 2-D Electrophoresis Gels, Thierry Rabilloud. Staining of Preparative 2-D Gels: Coomassie Blue and Imidazole-Zinc Negative Staining, Neil M. Matsui, Diana M. Smith-Beckerman, and Lois B. Epstein. Electroblotting of Proteins from 2-D Polyacrylamide Gels, Michael J. Dunn. Detection of Total Proteins on Western Blots of 2-D Polyacrylamide Gels, Michael J. Dunn. Protein Detection Using Reversible Metal Chelate Stains, Wayne F. Patton, Mark J. Lim, and David Shepro. Gylcoprotein Detection of 2-D Separated Proteins, Nicolle H. Packer, Malcolm S. Ball, and Peter L. Devine. Image Acquisition in 2-D Electrophoresis, Wayne F. Patton, Mark J. Lim, and David Shepro. Computer Analysis of 2-D Images, Ron D. Appel and Denis F. Hochstrasser. 2-D Databases on the World Wide Web, Ron D. Appel, Amos Bairoch, and Denis F. Hochstrasser. Comparing 2-D Electrophoresis Gels Across Internet Databases, Peter F. Lemkin. Constructing a 2-D Database for the World Wide Web, Ron D. Appel, Christine Hoogland, Amos Bairoch, and Denis F. Hochstrasser. Absolute Quantitation of 2-D Protein Spots, Steven P. Gygi and Ruedi Aebersold. Generating a Bacterial Genome Inventory: Identifying 2-D Spots by Comigrating Products of the Genome on 2-D Gels, Ruth A. VanBogelen. Immunoaffinity Identification of 2-DE Separated