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| Abbreviations | |
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| Preface | |
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| From genomics to proteomics | |
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| Introduction | |
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| The birth of large-scale biology | |
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| The genome, transcriptome and proteome | |
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| Functional genomics at the DNA and RNA levels | |
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| Transcriptomics | |
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| Large-scale mutagenesis | |
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| RNA interference | |
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| The need for proteomics | |
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| The scope of proteomics | |
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| Sequence and structural proteomics | |
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| Expression proteomics | |
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| Interaction proteomics | |
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| Functional proteomics | |
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| The challenges of proteomics | |
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| Strategies for protein separation | |
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| Introduction | |
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| Protein separation in proteomics - general principles | |
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| Principles of two-dimensional gel electrophoresis | |
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| General principles of protein separation by electrophoresis | |
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| Separation according to charge but not mass - isoelectric focusing | |
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| Separation according to mass but not charge - SDS-PAGE | |
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| Two-dimensional gel electrophoresis in proteomics | |
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| Limitations of 2DGE in proteomics | |
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| Improving the resolution of 2DGE | |
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| Improving the sensitivity of 2DGE | |
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| The representation of proteins on 2D-gels | |
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| The automation of 2DGE | |
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| Principles of liquid chromatography in proteomics | |
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| General principles of protein and peptide separation by chromatography | |
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| Affinity chromatography | |
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| Ion exchange chromatography | |
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| Reverse-phase chromatography | |
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| Size exclusion chromatography | |
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| Multidimensional liquid chromatography | |
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| Comparison of multidimensional liquid chromatography and 2DGE | |
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| Strategies for multidimensional liquid chromatography in proteomics | |
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| Strategies for protein identification | |
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| Introduction | |
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| Protein identification with antibodies | |
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| Determining protein sequences by chemical degradation | |
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| Complete hydrolysis | |
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| Protein sequencing by Edman degradation | |
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| Edman degradation in proteomics | |
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| Mass spectrometry in proteomics - basic principles and instrumentation | |
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| Overview | |
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| The importance of intact peptide ions | |
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| Instrumentation | |
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| Protein identification using data from mass spectrometry | |
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| Peptide mapping (peptide mass fingerprinting) | |
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| Advantages and limitations of peptide mass fingerprinting | |
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| Fragment ion analysis | |
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| Determining protein sequences de novo by mass spectrometry | |
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| Strategies for protein quantitation | |
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| Introduction | |
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| Quantitive proteomics with standard 2D gels | |
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| Image acquisition from 2D gels | |
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| Spot detection, quantitation and comparison | |
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| Multiplexed proteomics | |
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| Difference gel electrophoresis | |
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| Parallel analysis with multiple dyes | |
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| Quantitative proteomics with mass spectrometry | |
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| ICAT reagents | |
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| Nonselective labeling of peptides after digestion | |
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| Isotape tagging in vivo | |
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| Mass-coded abundance tags | |
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| Proteomics and the analysis of protein sequences | |
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| Introduction | |
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| Protein families and evolutionary relationships | |
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| Evolutionary relationships between proteins | |
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| Predicting function from sequence | |
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| Basic principles of protein sequence comparison | |
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| Identity and similarity between protein sequences | |
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| Substitution score matrices | |
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| Pairwise similarity searching | |
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| The significance of sequence alignments | |
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| Multiple alignments | |
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| Finding more distant relationships | |
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| PSI-BLAST | |
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| Pattern recognition | |
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| Pitfalls of functional annotation by similarity searching | |
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| Alternative methods for functional annotation | |
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| Structural proteomics | |
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| Introduction | |
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| The value of protein structures in proteomics | |
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| Structure-function concordance | |
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| Structure-function nonconcordance | |
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| Techniques for solving protein structures | |
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| X-ray crystallography | |
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| Nuclear magnetic resonance spectroscopy | |
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| Additional methods for structural analysis | |
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| Techniques for modeling protein structures | |
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| Predicting protein secondary structures from sequence data | |
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| Tertiary structure prediction by comparative modeling | |
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| Ab initio prediction methods | |
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| Fold recognition (threading) | |
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| Comparing protein structures | |
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| The structural classification of proteins | |
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| Structural proteomics: initiatives and results | |
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| Interaction proteomics | |
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| Introduction | |
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| Principles of protein-protein interaction analysis | |
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| Genetic methods | |
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| Bioinformatic methods | |
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| Affinity-based biochemical methods | |
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| Physical methods | |
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| Library-based methods for the global analysis of binary interactions | |
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| Standard expression libraries | |
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| Phage interaction display | |
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| The yeast two-hybrid system | |
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| Interaction proteomics using the yeast two-hybrid system | |
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| Matrix screening | |
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| Pooled matrix screening | |
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| Random library screening | |
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| Limitations of the yeast two-hybrid system | |
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| Systematic complex analysis by mass spectrometry | |
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| Protein localization in proteomics | |
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| Protein interaction maps | |
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| Proteins and small molecules | |
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| Protein modification in proteomics | |
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| Introduction | |
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| Phosphoproteomics | |
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| Overview of protein phosphorylation | |
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| Sample preparation for phosphoprotein analysis | |
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| Detection of phosphoproteins after protein separation | |
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| Identification of phosphorylated residues | |
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| Identification of phosphoproteins and prediction of phosphorylated sites | |
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| Quantitative phosphoproteomics | |
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| Glycoproteomics | |
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| Glycoproteins | |
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| The role of glycoproteins in the cell | |
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| Glycoanalysis | |
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| Separation and detection of glycoproteins | |
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| Enrichment of glycoproteins | |
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| High-throughput identification and characterization of glycoproteins | |
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| Ubiquitinomics | |
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| Protein chips and functional proteomics | |
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| Introduction | |
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| Different types of protein chips | |
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| Antibody arrays | |
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| Alternative capture agents | |
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| Antigen arrays | |
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| Broad-specificity capture chips | |
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| Functional protein chips | |
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| The manufacture of protein chips | |
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| Detecting and quantifying proteins bound to protein chips | |
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| Methods that require labels | |
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| Label-free methods | |
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| Emerging protein chip technologies | |
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| Bead and particle arrays in solution | |
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| Cell and tissue arrays | |
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| Applications of proteomics | |
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| Introduction | |
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| Medical proteomics-disease diagnosis | |
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| Biomarkers | |
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| Biomarker discovery using 2DGE and mass spectrometry | |
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| Biomarker discovery and pattern profiling using protein chips | |
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| Pharmaceutical proteomics-drug development | |
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| The role of proteomics in target identification | |
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| Proteomics and target validation | |
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| Proteomics in the development of lead compounds | |
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| Proteomics and clinical development | |
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| Proteomics and plant biotechnology | |
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| Proteomics in plant breeding and genetics | |
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| Proteomics for the analysis of genetically modified plants | |
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| Proteomics and the analysis of secondary metabolism | |
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| Index | |