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• Title:Principles of proteomics / Richard M. Twyman.
  
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• Author/Creator:Twyman, Richard M.
  
• Published/Created:New York : Garland Science, ©2014.
  

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  • Location:WOODWARD LIBRARY stacksWhere is this?
    
  • Call Number: QU460 .T975p 2014
    
  • Number of Items:1
    
  • Status:Available
    

   
• Library of Congress Subjects:Proteomics.
  Proteins.
  
• Medical Subjects: Proteomics.
  Proteins--analysis.
  
• Edition:Second edition.
  
• Description:xi, 260 pages : color illustrations ; 28 cm
  
• Summary:'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.
  
• Notes:Includes bibliographical references and index.
  
• ISBN:9780815344728 (alk. paper)
  0815344724 (alk. paper)
  
• Contents:Machine generated contents note: 1.1. Introduction
  1.2. Birth Of Large-Scale Biology And The "Omics" Era
  1.3. Genome, Transcriptome, Proteome, And Metabolome
  1.4. Functional Genomics
  Transcriptomics is the systematic, global analysis of mRNA
  Large-scale mutagenesis and interference can also determine the functions of genes on a global scale
  1.5. Need For Proteomics
  1.6. Scope Of Proteomics
  Protein identification and quantitation are the most fundamental aspects of proteomic analysis
  Important functional data can be gained from sequence and structural analysis
  Interaction proteomics and activity-based proteomics can help to link proteins into functional networks
  1.7. Current Challenges In Proteomics
  2.1. Introduction
  2.2. General Principles Of Protein Separation In Proteomics
  2.3. Principles Of Two-Dimensional Gel Electrophoresis
  Electrophoresis separates proteins by mass and charge
  Isoelectric focusing separates proteins by charge irrespective of mass
  SDS-PAGE separates proteins by mass irrespective of charge
  2.4. Application Of 2DGE In Proteomics
  four major advantages of 2DGE are robustness, reproducibility, visualization, and compatibility with downstream microanalysis
  four major limitations of 2DGE are resolution, sensitivity, representation, and compatibility with automated protein analysis
  resolution of 2DGE can be improved with giant gels, zoom gels, and modified gradients, or by pre-fractionating the sample
  sensitivity of 2DGE depends on the visualization of minor protein spots, which can be masked by abundant proteins
  representation of hydrophobic proteins is an intractable problem reflecting the buffers required for isoelectric focusing
  Downstream mass spectrometry requires spot analysis and picking
  2.5. Principles Of Multidimensional Liquid Chromatography
  Protein and peptide separation by chromatography relies on differing affinity for stationary and mobile phases
  Affinity chromatography exploits the specific binding characteristics of proteins and/or peptides
  Size exclusion chromatography sieves molecules on the basis of their size
  Ion exchange chromatography exploits differences in net charge
  Reversed-phase chromatography and hydrophobic interaction chromatography exploit the affinity between peptides and hydrophobic resins
  2.6. Multidimensional Liquid Chromatography Strategies In Proteomics
  Multidimensional liquid chromatography is more versatile and more easily automated than 2DGE but lacks a visual dimension
  most useful MDLC systems achieve optimal peak capacity by exploiting orthogonal separations that have internally compatible buffers
  MudPIT shows how MDLC has evolved from a laborious technique to virtually hands-free operation
  RP-RPLC and HILIC-RP systems offer advantages for the separation of certain types of peptide mixtures
  Affinity chromatography is combined with MDLC to achieve the simplification of peptide mixtures
  3.1. Introduction
  3.2. Protein Identification With Antibodies
  3.3. Determination Of Protein Sequences By Chemical Degradation
  Complete hydrolysis allows protein sequences to be inferred from the content of the resulting amino acid pool
  Edman degradation was the first general method for the de novo sequencing of proteins
  Edman degradation was the first protein identification method to be applied in proteomics, but it is difficult to apply on a large scale
  3.4. Mass Spectrometry-Basic Principles And Instrumentation
  Mass spectrometry is based on the separation of molecules according to their mass/charge ratio
  integration of mass spectrometry into proteomics required the development of soft ionization methods to prevent random fragmentation
  Controlled fragmentation is used to break peptide bonds and generate fragment ions
  Five principal types of mass analyzer are commonly used in proteomics
  3.5. Protein Identification Using Data From Mass Spectra
  Peptide mass fingerprinting correlates experimental and theoretical intact peptide masses
  Shotgun proteomics can be combined with database searches based on uninterpreted spectra
  MS/MS spectra can be used to derive protein sequences de novo
  4.1. Introduction
  4.2. Quantitative Proteomics Based On 2DGE
  quantitation of proteins in two-dimensional gels involves the creation of digital data from analog images
  Spot detection, quantitation, and comparison can be challenging without human intervention
  4.3. Multiplexed In-Gel Proteomics
  Difference in-gel electrophoresis involves the simultaneous separation of comparative protein samples labeled with different fluorophores
  Parallel analysis with multiple dyes can also be used to identify particular structural or functional groups of proteins
  4.4. Quantitative Mass Spectrometry
  Label-free quantitation may be based on spectral counting or the comparison of signal intensities across samples in a narrow m/z range
  Label-based quantitation involves the incorporation of labels that allow corresponding peptides in different samples to be identified by a specific change in mass
  ICAT reagents are used for the selective labeling of proteins or peptides
  Proteins and peptides can also be labeled nonselectively
  Isobaric tagging allows protein quantitation by the detection of reporter ions
  Metabolic labeling introduces the label before sample preparation but is limited to simple organisms and cultured cells
  5.1. Introduction
  5.2. Protein Families And Evolutionary Relationships
  Evolutionary relationships between proteins are based on homology
  function of a protein can often be predicted from its sequence
  5.3. Principles Of Protein Sequence Comparison
  Protein sequences can be compared in terms of identity and similarity
  Homologous sequences are found by pairwise similarity searching
  Substitution score matrices rank the importance of different substitutions
  Sequence alignment scores depend on sequence length
  Multiple alignments provide more information about key sequence elements
  5.4. Strategies To Find More Distant Relationships
  PSI-BLAST uses sequence profiles to carry out iterative searches
  Pattern recognition methods incorporate conserved sequence signatures
  5.5. Risk Of False-Positive Annotations
  6.1. Introduction
  6.2. Structural Genomics And Structure Space
  Coverage of structure space is currently uneven
  Structure and function are not always related
  6.3. Techniques For Solving Protein Structures
  X-ray diffraction requires well-ordered protein crystals
  NMR spectroscopy exploits the magnetic properties of certain atomic nuclei
  Additional methods for structural analysis mainly provide supporting data
  6.4. Protein Structure Prediction
  Structural predictions can bridge the gap between sequence and structure
  Protein secondary structures can be predicted from sequence data
  Tertiary structures can be predicted by comparative modeling if a template structure is available
  Ab initio prediction methods attempt to construct structures from first principles
  Fold recognition (threading) is based on similarities between nonhomologous folds
  6.5. Comparison Of Protein Structures
  6.6. Structural Classification Of Proteins
  6.7. Global Structural Genomics Initiatives
  7.1. Introduction
  7.2. Methods To Study Protein-Protein Interactions
  Genetic methods suggest interactions from the combined effects of two mutations in the same cell or organism
  Protein interactions can be suggested by comparative genomics and homology transfer
  Affinity-based biochemical methods provide direct evidence that proteins can interact
  Interactions between proteins in vitro and in vivo can be established by resonance energy transfer
  Surface plasmon resonance can indicate the mass of interacting proteins
  7.3. Library Based Methods For The Global Analysis Of Binary Interactions
  7.4. Two-Hybrid/protein Complementation Assays
  yeast two-hybrid system works by assembling a transcription factor from two inactive fusion proteins
  Several large-scale interaction screens have been carried out using different yeast two-hybrid screening strategies
  Conventional yeast two-hybrid screens have a significant error rate
  7.5. Modified Two-Hybrid Systems For Membrane, Cytosolic, And Extracellular Proteins
  7.6. Bacterial And Mammalian Two-Hybrid Systems
  7.7. Lumier And Mappit High-Throughput Two-Hybrid Platforms
  7.8. Adapted Hybrid Assays For Different Types Of Interactions
  7.9. Systematic Complex Analysis By Tandem Affinity Purification-Mass Spectrometry
  7.10. Analysis Of Protein Interaction Data
  7.11. Protein Interaction Maps
  7.12. Protein Interactions With Small Molecules
  8.1. Introduction
  8.2. Methods For The Detection Of Post Translational Modifications
  8.3. Enrichment Strategies For Modified Proteins And Peptides
  8.4. Phosphoproteomics
  Protein phosphorylation is a key regulatory mechanism
  Separated phosphoproteins can be detected with specific staining reagents
  Sample preparation for phosphoprotein analysis typically involves enrichment using antibodies or strongly cationic chromatography resins
  8.5. Analysis Of Phosphoproteins By Mass Spectrometry
  combination of Edman degradation and mass spectrometry can be used to map phosphorylation sites
  Intact phosphopeptide ions can be identified by MALDI-TOF mass spectrometry
  Phosphopeptides yield diagnostic marker ions and neutral loss products
  8.6. Quantitative Analysis Of Phosphoproteins
  8.7. Glycoproteomics
  Contents note continued: Glycoproteins represent more than half of the eukaryotic proteome
  Glycans play important roles in protein stability, activity, and localization, and are important indicators of disease
  Conventional glycoanalysis involves the use of enzymes that remove specific glycan groups and the separation of glycoproteins by electrophoresis
  Glycoprotein-specific staining allows the glycoprotein to be studied by 2DGE
  There are two principal methods for glycoprotein enrichment that have complementary uses
  Mass spectrometry is used for the high-throughput identification and characterization of glycoproteins
  9.1. Introduction
  9.2. Evolution Of Protein Microarrays
  9.3. Different Types Of Protein Microarrays
  Analytical, functional, and reverse microarrays are distinguished by their purpose and the nature of the interacting components
  Analytical microarrays contain antibodies or other capture reagents
  Functional protein microarrays can be used to study a wide range of biochemical functions
  9.4. Manufacture Of Functional Protein Microarrays-Protein Synthesis
  Proteins can be synthesized by the parallel construction of many expression vectors
  Cell-free expression systems allow the direct synthesis of protein arrays in situ
  9.5. Manufacture Of Functional Protein Microarrays-Protein Immobilization
  9.6. Detection Of Proteins On Microarrays
  Methods that require labels can involve either direct or indirect detection
  Label-free methods do not affect the intrinsic properties of interacting proteins
  9.7. Emerging Protein Chip Technologies
  Bead and particle arrays in solution represent the next generation of protein microarrays
  Cell and tissue arrays allow the direct analysis of proteins in vivo
  10.1. Introduction
  10.2. Diagnostic Applications Of Proteomics
  Proteomics is used to identify biomarkers of disease states
  Biomarkers can be discovered by finding plus/minus or quantitative differences between samples
  More sensitive techniques can be used to identify biomarker profiles
  10.3. Applications Of Proteomics In Drug Development
  Proteomics can help to select drug targets and develop lead compounds
  Proteomics is also useful for target validation
  Chemical proteomics can be used to select and develop lead compounds
  Proteomics can be used to assess drug toxicity during clinical development
  10.4. Proteomics In Agriculture
  Proteomics provides novel markers in plant breeding and genetics
  Proteomics can be used for the analysis of genetically modified plants
  10.5. Proteomics In Industry-Improving The Yield Of Secondary Metabolism.