PROTIDES OF THE BIOLOGICAL FLUIDS
CONTENTS PART I: SAMPLE PREPARATION BASICS 1 MECHANICAL/PHYSICAL METHODS OF CELL DISRUPTION AND TISSUE HOMOGENIZATION 2 BACTERIA AND YEAST CELL DISRUPTION USING LYTIC ENZYMES 2 3 SAMPLE SOLUBLIZATION BUFFERS FOR TWO-DIMENSIONAL ELECTROPHORESIS 3 4 QUANTITATION OF PROTEIN IN SAMPLES PREPARED FOR 2-D ELECTROPHORESIS 4 5 REMOVAL OF INTERFERING SUBSTANCES IN SAMPLES PREPARED FOR TWO-DIMENSIONAL (2-D) ELECTROPHORESIS 4 6 PROTEIN CONCENTRATION BY HYDROPHILIC INTERACTION CHROMATOGRAPHY COMBINED WITH SOLID PHASE EXTRACTION 6 PART II: PROTEIN LABELING TECHNIQUES 7 DIFFERENCE GEL ELECTROPHORESIS BASED ON LYS/CYS TAGGING 6 8 ISOTOPE-CODED TWO-DIMENSIONAL MAPS: TAGGING WITH DEUTERATED ACRYLAMIDE AND 2-VINYLPYRIDINE 8 9 STABLE ISOTOPE LABELING BY AMINO ACIDS IN CELL CULTURE (SILAC) 9 10 ICPL—ISOTOPE-CODED PROTEIN LABEL 1 0 11 RADIOLABELING FOR TWO-DIMENSIONAL GEL ANALYSIS 1 1 PART III: FRACTIONATION OF PROTEINS BY CHEMICAL REAGENTS AND CHROMATOGRAPHY 12 SEQUENTIAL EXTRACTION OF PROTEINS BY CHEMICAL REAGENTS 1 2 13 REDUCING SAMPLE COMPLEXITY BY RP-HPLC: BEYOND THE TIP OF THE PROTEIN EXPRESSION ICEBERG 1 3 14 ENRICHING BASIC AND ACIDIC RAT BRAIN PROTEINS WITH ION EXCHANGE MINI SPIN COLUMNS BEFORE TWO-DIMENSIONAL GEL ELECTROPHORESIS 1 4 15 REDUCING THE COMPLEXITY OF THE ESCHERICHIA COLI PROTEOME BY CHROMATOGRAPHY ON REACTIVE DYE COLUMNS 1 5 16 REDUCING SAMPLE COMPLEXITY IN PROTEOMICS BY CHROMATOFOCUSING WITH SIMPLE BUFFER MIXTURES 1 7 17 FRACTIONATION OF PROTEINS BY IMMOBILIZED METAL AF?NITY CHROMATOGRAPHY 1 9 18 FRACTIONATION OF PROTEINS BY HEPARIN CHROMATOGRAPHY 2 0 PART IV: FRACTIONATION OF PROTEINS BY ELECTROPHORESIS METHODS 19 FRACTIONATION OF COMPLEX PROTEIN MIXTURES BY LIQUID-PHASE ISOELECTRIC FOCUSING 2 1 20 MICROSCALE ISOELECTRIC FOCUSING IN SOLUTION 2 2 21 PREFRACTIONATION, ENRICHMENT, DESALTING AND DEPLETING OF LOW VOLUME AND LOW ABUNDANCE PROTEINS AND PEPTIDES USING THE MF10 2 4 22 SAMPLE PREFRACTIONATION IN GRANULATED SEPHADEX IEF GELS 2 6 23 FREE-FLOW ELECTROPHORESIS SYSTEM FOR PLASMA PROTEOMIC APPLICATIONS 2 7 24 PROTEIN FRACTIONATION BY PREPARATIVE ELECTROPHORESIS 2 8 PART V: ENRICHMENT STRATEGIES FOR ORGANELLES, MULTIPROTEIN COMPLEXES, AND SPECI?C PROTEIN CLASSES 25 ISOLATION OF ENDOCITIC ORGANELLES BY DENSITY GRADIENT CENTRIFUGATION 2 9 26 ISOLATION OF HIGHLY PURE RAT LIVER MITOCHONDRIA WITH THE AID OF ZONE-ELECTROPHORESIS IN A FREE FLOW DEVICE (ZE-FFE) 3 1 27 ISOLATION OF PROTEINS AND PROTEIN COMPLEXES BY IMMUNOPRECIPITATION 3 3 28 ISOLATION OF PHOSPHOPROTEINS 3 4 29 GLYCOPROTEIN ENRICHMENT THROUGH LECTIN AF?NITY TECHNIQUES 3 5 30 ISOLATION OF BACTERIAL CELL MEMBRANES PROTEINS USING CARBONATE EXTRACTION 3 7 31 ENRICHMENT OF MEMBRANE PROTEINS BY PARTITIONING IN DETERGENT/POLYMER AQUEOUS TWO-PHASE SYSTEMS 3 8 32 THE ISOLATION OF DETERGENT-RESISTANT LIPID RAFTS FOR TWO-DIMENSIONAL ELECTROPHORESIS 3 9 33 ISOLATION OF MEMBRANE PROTEIN COMPLEXES BY BLUE NATIVE ELECTROPHORESIS 4 0 34 TISSUE MICRODISSECTION 4 1