The Proteome Revisited Theory and practice of all relevant electrophoretic steps 1st Edition by A Stoyanov, M Zhukov, Pier Giorgio Righetti ISBN 0080518966 9780080518961

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ISBN 10: 0080518966 
ISBN 13: 9780080518961
Author: A Stoyanov, M Zhukov, Pier Giorgio Righetti

The book deals with the theory and practice of all electrophoretic steps leading to proteome analysis, i.e. isoelectric focusing (including immobilized pH gradients), sodium dodecyl sulphate electrophoresis (SADS-PAGE) and finally two-dimensional maps. It is a reasoned collection of all modern, relevant, up-to-date methodologies leading to successful fractionation, analysis and characterization of every polypeptide spot in 2-D map analysis. It includes chapters on the most sophisticated mass spectrometry developments and it helps the reader in navigating through the most important databases in proteome analysis, including step by step tours in selected sites. Yet, this book’s unique strength and feature is the fact that it combines not only practice (in common with any other book on this topic) but also theory, by giving a detailed treatment on the most advanced theoretical treatments of steady-state techniques, such as isoelectric focusing and immobilized pH gradients. A lot of this theory is newly developed and presented to the public for the first time. Thus, this book should satisfy not only the needs of every day practitioners, but also the desires of the most advanced theoreticians in the field, who will surely appreciate the novel theories presented here

The Proteome Revisited Theory and practice of all relevant electrophoretic steps 1st Table of contents:

Part I: Isoelectric Focussing: Fundamentals. Perspectives and Limits. Optimization of the Separation
Introduction

Part I.I: Isoelectric Focussing: Fundamentals
Chapter 1. Electrolyte Dissociation in Water Solution. Simple Electrolytes
1.1. Introduction
1.2. Stepwise and parallel dissociation schemes for a bivalent protolyte
1.3. Relative concentration of different protolyte forms for stepwise and parallel schemes
1.4. Hydrogen ions concentration and buffer capacity
1.5. Ionisation coefficient
1.6. Isoelectric point
1.7. Mobility of protolyte molecule
1.8. Non-additive sum for buffer capacity in case of stepwise dissociation
1.9. Non-amphoteric compounds and buffer capacity in ‘isoprotic state
1.10. Notations
1.11. References

Chapter 2. Dissociation of Polyvalent Electrolytes
2.1. Introduction
2.2. Acid–base equilibria, macroscopic and microscopic constants
2.3. Dissociation schemes of a hybrid type
2.4. Proton transfer tautomerism
2.5. Schemes with independent dissociation
2.6. Titration curve modelling
2.7. Linderstrøm-Lang equation
2.8. Calculation of the complete set of microconstants
2.9. Relative concentration of microstates for a homopolymer (independent dissociation)
2.10. Notation
2.11. References

Chapter 3. Kinetic Aspects of Acid–Base Equilibria
3.1. Introduction
3.2. Life-time of microscopic states
3.3. Relaxation of the ionic atmosphere
3.4. Modelling of the electrophoretic flux, electrophoretic mobility and conductivity
3.5. References

Chapter 4. Natural pH Gradients
4.1. Introduction
4.2. Simplest examples of natural pH gradients
4.3. pH gradients created with a multi-component mixture of amphoteric compounds
4.4. References

Chapter 5. Immobilised pH Gradients
5.1. Classical immobilised pH gradients created with linear density gradient
5.2. Linear pH gradients with non-linear gradients of concentration
5.3. Buffering and conductivity properties of immobilised pH gradients
5.4. Some characteristic features of electrophoresis in gel media with immobilised electric charge
5.5. Notation
5.6. References

Chapter 6. Steady-State IEF
6.1. Introduction
6.2. Steady-state concentration distribution with an assumption of no sample–buffer interaction
6.3. The influence of the focussing sample on gradient properties
6.4. References

Chapter 7. The Dynamics of Isoelectric Focussing
7.1. Introduction
7.2. Diffusionless approximation
7.3. The evaluation of focussing time
7.4. References

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Part I.II: Optimization of the Electrophoretic Separation

Chapter 8. Buffering Capacity
8.1. Introduction
8.2. Buffer capacity and buffer resource
8.3. Buffer properties of solutions of proteins and nucleic acids
8.4. Biopolymers as titration agents
8.5. References

Chapter 9. Optimisation of Electrophoretic Separation
9.1. Optimisation of electrophomtic separation using pH–charge relationship
9.2. Dependence of mobility on molecular mass in free solution
9.3. Isoelectric buffers. The concept of ‘normalised β/λ ratio’
9.4. References

Chapter 10. Two-Dimensional Methods
10.1. Two-dimensional electrophoresis
10.2. Other two-dimensional separations
10.3. Mobility versus pH curves
10.4. References

Chapter 11. Limitations of the Method of Isoelectric Focussing
11.1. Introduction
11.2. Ways of generating pH gradients
11.3. Intrinsic limits of IEF
11.4. Microheterogeneity of proteins and other biopolymers
11.5. References

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Part II Methodology

Chapter 12. Conventional Isoelectric Focussing in Gel Slabs and Capillaries and Immobilised pH Gradients
12.1. Introduction
12.2. Conventional isoelectric focussing in amphoteric buffers
12.3. Immobilised pH gradients
12.4. Capillary isoelectric focussing (cIEF)
12.5. Separation of peptides and proteins by CZE in isoelectric buffers
12.6. Conclusions
12.7. References

Chapter 13. Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE)
13.1. Introduction
13.2. SDS-protein complexes: a refinement of the model
13.3. Theoretical background of Mr measurement by SDS-PAGE
13.4. Methodology
13.5. Gel casting and buffer systems
13.6. Blotting procedures
13.7. Conclusions
13.8. References

Chapter 14. Two-Dimensional Maps
14.1. Introduction
14.2. Some basic methodology pertaining to 2-D PAGE
14.3. Mass spectrometry in proteomics
14.4. Informatics and proteome: interrogating databases
14.5. Pre-fractionation tools in proteome analysis
14.6. Non-denaturing protein maps
14.7. References

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