Neuroproteomics

Part I: Introduction

1. Neuroproteomics: Deciphering Brain Function and Disorders

Ka Wan Li

Part II: Fractionation of Brain Regions, Organelles, and Protein Complexes

2. Dissection of Rodent Brain Regions

Sabine Spijker

3. Subcellular Fractionation of Brain Tissue Using Free Flow Electrophoresis

Markus Islinger, Joachim Kirsch, Sabine Angermüller, Ramona Rotaru, Afsaneh Abdolzade-Bavil, and Gerhard Weber

4. Isolation of Synapse Sub-Domains by Subcellular Fractionation Using Sucrose Density Gradient Centrifugation

Tatsuo Suzuki

5. Enrichment of Plasma Membranes from Small Brain Samples by Aqueous Polymer Two-Phase Systems

Jens Schindler

6. Identification and Characterization of Protein Complexes from Total Brain and Synaptoneurosomes: Heterogeneity of Molecular Complexes in Distinct Subcellular Domains

Silvia De Rubeis and Claudia Bagni

7. Analysis of Protein Complexes by 2D Blue Native/SDS-PAGE and Antibody-Shift Assay

Dong Yang, Xinyu Deng, Ying Jiang, and Fuchu He

Part III: Analytical Tools for Neuroproteomics

8. 2-Dimensional Gel Electrophoresis-Based Proteomic Analysis of Brain Synapses

Karl-Heinz Smalla and Ursula Wyneken

9. 2-Dimensional BAC-SDS Polyacrylamide Gel Electrophoresis for the Fractionation and Identification of Synaptic Vesicle Proteins and the Presynaptic Active Zone

Joern Barth and Walter Volknandt

10. iTRAQ-Based LC-LC MALDI TOF/TOF MS Quantitative Analysis of Membrane Proteins from Human Glioma

Uroš Rajčević

11. OFFGEL-Isoelectric Focusing Fractionation for the Analysis of Complex Proteome

Emilie Ernoult and Catherine Guette

12. A 1D-PAGE/LC-ESI Linear Ion Trap Orbitrap MS Approach for the Analysis of Synapse Proteomes and Synaptic Protein Complexes

Ning Chen, Roel C. vd Schors and August B. Smit

13. SDS-PAGE Immuno-Blot Analysis

Patricia Klemmer

14. Phosphoproteomics by Highly Selective IMAC Protocol

Chia-Feng Tsai, Yi-Ting Wang, Pei-Yi Lin, and Yu-Ju Chen

15. Global Analysis of Ubiquitination

David Meierhofer and Peter Kaiser

16. High-Throughput High-Content Functional Image Analysis of Neuronal Proteins Implicated in Parkinson’s Disease

Eva Blaas and Ronald E. van Kesteren

Part IV: Analysis of Specific Brain Tissues and Fluid

17. Neuropeptidomics of the Mammalian Brain

Fang Xie, Elena V. Romanova, and Jonathan V. Sweedler

18. In-Depth Analysis of the Cerebrospinal Fluid Proteome and Biomarker Discovery: Abundant Protein Depletion Sample Pretreatment Method

Silvina A. Fratantoni and Connie R. Jimenez

19. Lipidomics of the Nervous System: Phospholipidomics by Liquid Chromatography Coupled to Mass Spectrometry or Tandem Mass Spectrometry

Su Chen

Part V: Bioinformatics

20. Bioinformatics Procedures for Analysis of Quantitative Proteomics Experiments Using iTRAQ

Pim van Nierop and Maarten Loos

21. Statistical Analysis of Spectral Count Data Generated by Label-Free Tandem Mass Spectrometry-Based P

In the past few years, the application of proteomics to examine the molecular mechanisms underlying (mal-)functioning of the nervous system and brain disorders has risen steeply, which in many cases has yielded novel insights. As neuroproteomics is a new research field involving the use of a number of high-end analytical instruments and technologies, both promises and pitfalls may not be well appreciated by the researchers, and the design of a proper proteomics experiment may not be obvious. Neuroproteomics brings together a collection of detailed protocols written by experienced professionals in the field in order to cover aspects of various dimensions of this new technology, together with some established methods that have supporting roles in the workflow of neuroproteomics. Written for the popular Neuromethods series, the chapters in this book contain step-by-step, easy to follow instruction along with practical tips and key implementation advice essential for successful implementation of the techniques.

Authoritative and cutting-edge, Neuroproteomics will be of great assistance to all researchers seeking to design and execute their own proteomics experiments in an optimal way and continue moving forward this exciting area of study.