2-D proteome analysis protocols

2-D protein gel electrophoresis. An overview -- Solubilization of proteins in 2-D electrophoresis. An outline -- Preparation of escherichia coli samples for 2-D gel analysis -- Preparing 2-D protein extracts from yeast -- 2-D protein extracts from drosophila melanogaster -- Preparing 2-D protein extracts from caenorhabditis elegans -- Eukaryotic cell labeling and preparation for 2-D -- Differential detergent fractionation of eukaryotic cells. Analysis by two-dimensional gel electrophoresis -- Fractionated extraction of total tissue proteins from mouse and human for 2-D electrophoresis -- Preparation and solubilization of body fluids for 2-D -- 2-D electrophoresis of plant proteins -- Quantifying protein in 2-D page solubilization buffers -- Measuring the radioactivity of 2-D protein extracts -- Advantages of carrier ampholyte ief -- 2-D electrophoresis using carrier ampholytes in the first dimension (IEF) -- Nonequilibrium ph gel electrophoresis (nephge) -- High-resolution, 2-D protein electrophoresis using nondedicated equipment -- Large-gel 2-D electrophoresis -- Advantages of immobilized ph gradients -- Casting immobilized ph gradients (ipgs) -- Analytical ipg-dalt -- LPG-dalt of very alkaline proteins -- Running preparative carrier ampholyte and immobilized ph gradient IEF gels for 2-D -- In-gel sample rehydration of immobilized ph gradient -- High-resolution, IPG-based, mini two-dimensional gel electrophoresis -- Horizontal SDS-page for IPG-dalt -- Casting and running vertical slab-gel electrophoresis for 2d-page -- Nonreducing 2-D polyacrylamide gel electrophoresis -- 2-D diagonal gel electrophoresis -- 2-D phosphopeptide mapping -- Internal standards for 2-D -- Autoradiography of 2-D gels -- Double-label analysis -- Silver staining of 2-D electrophoresis gels -- Staining of preparative 2-D gels. Coomassie blue and imidazole-zinc negative staining -- Electroblotting of proteins from 2-D polyacrylamide gels -- Detection of total proteins on western blots of 2-D polyacrylamide gels -- Protein detection using reversible metal chelate stains -- Glycoprotein detection of 2-D separated proteins -- Image acquisition in 2-D electrophoresis -- Computer analysis of 2-D images -- 2-D databases on the world wide web -- Comparing 2-D electrophoretic gels across internet databases -- Constructing a 2-D database for the world wide web -- Absolute quantitation of 2-D protein spots -- Generating a bacterial genome inventory. Identifying 2-D spots by comigrating products of the genome on 2-D gels -- Immunoaffinity identification of 2-De separated proteins -- 2-De spot amino acid analysis with 9-fluorenylmethyl chloroformate -- N-terminal amino acid sequencing of 2-De spots -- Characterizing proteins from 2-De gels by internal sequence analysis of peptide fragments. Strategies for microsample handling -- Obtaining molecular weights of proteins and their cleavage products by directly combining gel electrophoresis with mass spectrometry -- Identification of proteins by matrix-assisted laser desorption/ionization mass spectrometry using peptide and fragment ion masses -- Sample preparation methods for mass spectrometric peptide mapping directly from 2-De gels -- Protein identification and analysis tools in the expasy server -- Automated protein identification using microcolumn liquid chromatography-tandem mass spectrometry -- Peptide sequencing of 2-De gel-isolated proteins by nanoelectrospray tandem mass spectrometry