Abbreviations.

List of Contributors.

Colour Plates.

1 Protein Purification (Richard R. Burgess).

1.1 Introduction.

1.2 Types of Molecular Interactions and Variables that Affect Them.

1.3 Protein Properties that can be Used as Handles for Purification.

1.4 Types of Separation Methods.

1.5 Protein Inactivation and How to Prevent It.

1.6 Protein Purification Strategy.

1.7 Overproducing Recombinant Proteins.

1.8 Refolding Proteins Solubilized from Inclusion Bodies.

2 Common Methods in Proteomics (Henning Urlaub, Mads Grønborg, Florian Richter, Timothy D. Veenstra, Thorsten M¨uller, Florian Tribl, Helmut E.Meyer and Katrin Marcus).

2.1 Introduction.

2.2 Protein Separation by Polyacrylamide Gel Electrophoresis.

2.3 Liquid Chromatography-Based Separation Techniques.

2.4 Mass Spectrometry and Data Analysis.

2.5 Protein QuantificationMethods.

2.6 Summary.

3 Proteomic Technologies for the Analysis of Protein Complexes (Ming Zhou and Timothy D. Veenstra).

3.1 Introduction.

3.2 Methods for Isolating Protein Complexes.

3.3 Techniques for Identifying Protein Complexes.

3.4 Yeast Two-Hybrid Screening.

3.5 FluorescenceMicroscopy.

3.5.1 Multi-Epitope-Ligand Cartography.

3.6 Conclusions.

4 Analysis of Membrane Protein Complexes by Blue Native-PAGE (Veronika Reisinger and Lutz Andreas Eichacker).

4.1 Introduction.

4.2 Protocols.

4.3 Outlook.

5 Current Approaches to Protein Structure Analysis (Andrew P. Turnbull and Udo Heinemann).

5.1 Bioinformatics.

5.2 Protein Production.

5.3 Purification.

5.4 Structure Determination by X-Ray Crystallography.

5.5 Structure-Based Drug Design.

5.6 Structure Determination by NMR.

6 Primer to Proteins Underlying Cellular Complexity and Function in the Nervous System (Kojiro Yano).

6.1 Molecular Complexity in Neurons.

6.2 Cellular Complexity in the Nervous System and Neuronal Cell Types.

6.3 Conclusion.

7 Proteome Analysis of Plasma Membranes (Hans Gerd Nothwang).

7.1 Introduction.

7.2 Protocols.

7.3 Outlook.

8 Proteome Analysis of Synaptic Vesicles (Mads Grønborg, Matthew Holt, Florian Richter, Shigeo Takamori, Dietmar Riedel, Reinhard Jahn and Henning Urlaub).

8.1 Introduction.

8.2 Protocols.

8.3 Summary and Outlook.

9 Proteomics Analysis of the Synapse (A.B. Smit and K.W. Li).

9.1 Introduction.

9.2 Protocols.

9.3 Outlook.

10 Peptidomics of the Nervous System (K.W. Li and A.B. Smit).

10.1 Introduction.

10.2 Protocols.

10.3 Outlook.

11 Analysis of PosttranslationalModifications (Daniel S. Spellman and Thomas A. Neubert).

11.1 Introduction.

11.2 Protocols.

11.3 Outlook.

12 Proteomics of Neurodegenerative Disorders (Thorsten M¨uller, Florian Tribl, Michael Hamacher, Andre van Hall, Helmut E. Meyer and Katrin Marcus).

12.1 Introduction.

12.2 History of Brain Proteomics.

12.3 Alzheimer's Disease.

12.4 Parkinson's Disease.

12.5 Administrative Realization of Neuroproteomics: The Brain Proteome Projects.

13 The Search for Protein Biomarkers of Neurobiological Diseases (Gary M. Muschik, Haleem J. Issaq and Timothy D. Veenstra).

13.1 Introduction.

13.2 Methodology.

13.3 Outlook.

14 Redox Proteomics: Applications to Age-Related Neurodegenerative Disorders (Rukhsana Sultana, Shelley F. Newman and D. Allan Butterfield).

14.1 Introduction.

14.2 Methods.

14.3 Future Directions.

15 Paranode Structure and Function (Yasuhiro Ogawa and Matthew N. Rasband).

15.1 Introduction.

15.2 Protocols.

15.3 Outlook.

Index.