Proteomics in drug research

From skillful handling of the wide range of technologies to successful applications in drug discovery -- this handbook has all the information professional proteomics users need.
Edited by experts working at one of the hot spots in European proteomic research, the numerous contributions by experts from the pharmaceutical industry and public proteomics consortia to provide the necessary perspective on current trends and developments in this exciting field.
Following an introductory chapter, the book moves on to proteomic technologies, such as protein biochips, protein-protein interactions, and proteome analysis in situ. The section on applications includes bioinformatics, Alzheimer's disease, neuroproteomics, plasma and T-cell proteomics, differential phosphoproteome analysis and biomarkers, as well as pharmacogenomics.
Invaluable reading for medicinal and pharmaceutical chemists, gene technologists, molecular biologists, and those working in the pharmaceutical industry.

Author Notes

All six editors are Researchers at the Medical Proteom-Center hosted by the University of Bochum (Germany). This international research center was established in 2002 under the leadership of Helmut E. Meyer, a co-founder of the Protagen AG. Professor Meyer is also initiator and coordinator of the Human Brain Proteome Project within the German National Genome Research Net (NGFN) as well as of the Brain Proteome Project within the Human Proteome Organisation (HUPO BPP).

A Personal Foreword

Preface

List of Contributors

I Introduction

1 Administrative Optimization of Proteomics Networks for Drug DevelopmentAndre van Hall and Michael Hamacher

1.1 Introduction

1.2 Tasks and Aims of Administration

1.3 Networking

1.4 Evaluation of Biomarkers

1.5 A Network for Proteomics in Drug Development

1.6 Realization of Administrative Networking: the Brain Proteome Projects

References

2 Proteomic Data Standardization, Deposition and ExchangeSandra Orchard and Henning Hermjakob and Manuela Pruess and Rolf Apweiler

2.1 Introduction

2.2 Protein Analysis Tools

2.3 Data Storage and Retrieval

2.4 The Proteome Standards Initiative

2.5 General Proteomics Standards (GPS)

2.6 Mass Spectrometry

2.7 Molecular Interactions

2.8 Summary

References

II Proteomic Technologies

3 Difference Gel Electrophoresis (DIGE): the Next Generation of Two-Dimensional Gel Electrophoresis for Clinical ResearchBarbara Sitek and Burghardt Scheibe and Klaus Jung and Alexander Schramm and Kai Stuhler

3.1 Introduction

3.2 Difference Gel Electrophoresis: Next Generation of Protein Detection in 2-DE.References

4 Biological Mass Spectrometry: Basics and Drug Discovery Related ApproachesBettina Warscheid

4.1 Introduction

4.2 Ionization Principles

4.3 Mass Spectrometric Instrumentation

4.4 Protein Identification Strategies

4.5 Quantitative Mass Spectrometry for Comparative and Functional Proteomics

4.6 Metabolic Labeling Approaches

4.7 Chemical Labeling Approaches

4.8 Quantitative MS for Deciphering Protein-Protein Interactions

4.9 Conclusions

References

5 Multidimensional Column Liquid Chromatography (LC) in Proteomics - Where Are We Now?Egidijus Machtejevas and Klaus K. Unger and Reinhard Ditz

5.1 Introduction

5.2 Why Do We Need MD-LC/MS Methods?

5.3 Basic Aspects of Developing a MD-LC/MS Method

5.4 Applications of MD-LC Separation in Proteomics - a Brief Survey

5.5 Sample Clean-Up: Ways to Overcome the "Bottleneck" in Proteome Analysis

5.6 Summary

References

6 Peptidomics Technologies and Applications in Drug ResearchMichael Schrader and Petra Budde and Horst Rose and Norbert Lamping and Peter Schulz-Knappe and Hans-Dieter Zucht

6.1 Introduction

6.2 Peptides in Drug Research

6.3 Development of Peptidomics Technologies

6.4 Applications of Differential Display Peptidomics

6.5 Outlook

References

7 Protein Biochips in the Proteomic FieldAngelika L??cking and Dolores J. Cahill

7.1 Introduction

7.2 Technological Aspects

7.3 Applications of Protein Biochips

7.4 Contribution to Pharmaceutical Research and Development

References

8 Current Developments for the In Vitro Characterization of Protein InteractionsDaniela Moll and Bastian Zimmermann and Frank Gesellchen and Friedrich W. Herberg

8.1 Introduction

8.2 The Model System: cAMP-Dependent Protein Kinase

8.3 Real-time Monitoring of Interactions Using SPR Biosensors

8.4 ITC in Drug Design

8.5 Fluorescence Polarization, a Tool for High-Throughput Screening

8.6 AlphaScr

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Author Notes

Table of Contents