Proteomics in practice : a guide to successful experimental design /
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| Author / Creator: | Westermeier, Reiner. |
|---|---|
| Edition: | 2nd completely rev. ed. |
| Imprint: | Weinheim : Wiley-VCH ; Chichester : John Wiley [distributor], c2008. |
| Description: | xx, 482 p. : ill. (some col.) ; 25 cm. |
| Language: | English |
| Subject: | |
| Format: | Print Book |
| URL for this record: | http://pi.lib.uchicago.edu/1001/cat/bib/7195388 |
Table of Contents:
- Preface
- Foreword
- Abbreviations, Symbols, Units
- Introduction
- 1. History
- 2. Critical Points
- 2.1. Challenges of the Protein Samples
- 2.1. Challenges of the Analysis Systems
- 3. Proteomics Strategies
- 3.1. Proteome Mapping
- 3.2. Differential Analysis
- 3.3. Time Point Experiments
- 3.4. Verification of Targets or Biomarkers
- 3.5. Integration of Results into Biological Context
- 3.6. Systems Biology
- 4. Concept of Experimental Planning
- 4.1. Biological Replicates
- 4.2. Pooling of Samples: Yes or No?
- 4.3. Pre-fractionation of Samples: Yes or No?
- 4.4. Which is the Best Workflow to Start With?
- Part I. Proteomics Technology
- 1. Electrophoretic Techniques
- 1.1. The Principle of Electrophoresis and Some Methodological Background
- 1.1.1. Free Flow Electrophoretic Methods
- 1.1.2. Gels for Electrophoretic Techniques
- 1.1.3. Electroendosmosis Effects
- 1.2. Polyacrylamide Gel Electrophoresis
- 1.2.1. The Polyacrylamide Gel
- 1.2.2. SDS Polyacrylamide Gel Electrophoresis
- 1.2.3. Blue Native Electrophoresis
- 1.2.4. Cationic Detergent Electrophoresis
- 1.3. Blotting
- 1.3.1. Electrophoretic Transfer
- 1.3.2. Protein Detection on the Membrane
- 1.4. Isoelectric Focusing
- 1.4.1. Theoretical Background
- 1.4.2. Preparation of IEF Gels
- 1.4.3. Isoelectric Focusing in Proteomics
- 1.5. Two-dimensional Electrophoresis
- 1.5.1. Sample Preparation
- 1.5.2. Pre-labeling of Proteins for Difference Gel Electrophoresis
- 1.5.3. First Dimension: Isoelectric Focusing in IPG Strips
- 1.5.4. Second Dimension: SDS Electrophoresis
- 1.5.5. Detection of Protein Spots
- 1.6. Image Analysis
- 1.6.1. Image Acquisition
- 1.6.2. Image Analysis and Evaluation
- 1.6.3. Use of 2-D Electrophoresis Data
- 1.7. Spot Handling
- 1.7.1. Spot Picking
- 1.7.2. Protein Cleavage
- 2. Liquid Chromatography Techniques
- 2.1. Basic Principles of Important Liquid Chromatography Techniques
- 2.1.1. Ion Exchange Chromatography
- 2.1.2. Reversed Phase Chromatography
- 2.1.3. Affinity Chromatography
- 2.1.4. Gel Filtration
- 2.2. Strategic Approach and General Applicability
- 2.3. Liquid Chromatography Techniques and Applications in Proteome Analysis
- 2.3.1. Peptide Separation
- 2.3.2. 2DLC Peptide Separation
- 2.3.3. Affinity Chromatography and LC-MS/MS
- 2.3.4. Protein Pre-fractionation
- 2.4. Practical Considerations and Application of LC-based Protein Pre-fractionation
- 2.4.1. Sample Extraction and Preparation
- 2.4.2. Experimental Setup
- 2.4.3. Ion Exchange Chromatography and Protein Pre-fractionation
- 2.4.4. Reversed Phase Chromatography and Protein Pre-fractionation
- 2.4.5. Fraction Size and Number of Fractions
- 2.5. Critical Review and Outlook
- 3. Mass Spectrometry
- 3.1. Ionization
- 3.1.1. Matrix Assisted Laser Desorption Ionization
- 3.1.2. Electrospray Ionization
- 3.2. Ion Separation
- 3.2.1. Time-of-Flight Analyzer
- 3.2.2. Triple Quadrupole Analyzer
- 3.2.3. Quadrupole Ion Trap
- 3.2.4. Quadrupole Time-of-Flight
- 3.2.5. Hybrid Triple Quadrupole Linear Ion Trap
- 3.2.6. TOF/TOF Analyzer
- 3.2.7. Fourier Transform Ion Cyclotron
- 3.2.8. Orbitrap
- 3.3. Generating MS Data for Protein Identification
- 3.3.1. Peptide Mass Fingerprint
- 3.3.2. Peptide Mass Fingerprint Combined With Composition Information
- 3.3.3. Peptide Mass Fingerprint Combined With Partial Sequence Information
- 3.3.4. Tandem Mass Spectrometry
- 3.4. Protein Characterization
- 3.4.1. Phosphorylation Analysis
- 3.4.2. Affinity Chromatography
- 3.4.3. Chemical Derivatization
- 3.4.4. Glycosylation
- 3.5. Protein Quantification Using Mass Spectrometry
- 3.5.1. Stable Isotope Labeling Approaches
- 3.5.2. Isotope-coded Affinity Tags
- 3.5.3. Stable Isotope Labeling with Amino Acids in Cell Culture
- 3.5.4. AQUA
- 3.5.5. iTRAQ
- 3.5.6. Non-labeling Software Approaches
- 3.6. MS Strategies
- 3.6.1. Bottom up Approach
- 3.6.2. Top down Approach
- 4. Functional Proteomics: Studies of Protein-Protein Interactions
- 4.1. Non-immunological Methods
- 4.1.1. Separation of Intact Multi-protein Complexes
- 4.1.2. Probing with Interaction Partners
- 4.1.3. Surface Plasmon Resonance
- 4.2. Antibody-based Techniques
- 4.2.1. Western Blotting and Dot Blots
- 4.2.2. Protein Microarrays
- Part II. Practical Manual of Proteome Analysis
- Equipment, Consumables, Reagents
- Step 1. Sample Preparation
- Step 2. Fluorescence Difference Gel Electrophoresis
- Step 3. Isoelectric Focusing
- Step 4. SDS Polyacrylamide Gel Electrophoresis
- Step 5. Scanning of Gels Containing Pre-labeled Proteins
- Step 6. Staining of Gels
- Step 7. Image Analysis and Evaluation of DIGE Gels
- Step 8. Spot Excision
- Step 9. Sample Destaining
- Step 10. Protein Digestion
- Step 11. Microscale Desalting and Concentrating of Sample
- Step 12. Chemical Derivatization of the Peptide Digest
- Step 13. MS Analysis
- Step 14. Calibration of MALDI-ToF MS
- Step 15. Preparing for a Database Search
- Part III. Trouble Shooting
- 1. Two-dimensional Electrophoresis
- 1.1. Sample Preparation
- 1.2. Isoelectric focusing in IGPG strips
- 1.3. SDS PAGE
- 1.4. Staining
- 1.5. DIGE Fluorescence Labeling
- 1.6. Results in 2-D Electrophoresis
- 2. Mass Spectrometry
- References
- Glossary of Terms
- Index
- Legal Statements
