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Principles of Proteomics

ISBN-10: 1859962734

ISBN-13: 9781859962732

Edition: 2004

Authors: Richard M. Twyman

List price: $97.00
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Description:

'Principles of Proteomics' covers the development of large-scale technologies for protein separation, isolation, detection and quantification. It provides a comprehensive introduction to this relatively new field.
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Book details

List price: $97.00
Copyright year: 2004
Publisher: Taylor & Francis Group
Publication date: 9/24/2004
Binding: Paperback
Pages: 266
Size: 6.75" wide x 9.50" long x 0.75" tall
Weight: 1.188
Language: English

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