Neuroproteomics. Methods and Protocols

About this book

With the development of polypeptide ionization processes for mass spectrometry and the rapid processing of large-scale datasets with bioinformatics, researchers now have the tools necessary to propel neuroproteomics research to new levels. In Neuroproteomics: Methods and Protocols, experts in the neurological and analytical sciences present experimental details for applying proteomics to the study of the central nervous system (CNS) and its dysfunction through trauma and disease. Divided into four convenient sections, this collection covers CNS animal models used for neuroproteomics research, methods for separating and analyzing discrete subcomponents of the neuroproteome, large-scale approaches for CNS proteome characterization and quantification, as well as methods that evaluate biofluids and translate neuroproteomic results into clinical platforms. As a volume in the highly successful Methods in Molecular Biology™ series, chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Neuroproteomics: Methods and Protocols includes the clear "how-to" information needed to critically assess what can be accomplished in the field and how to best perform and evaluate neuroproteomic experiments in one’s own research.

Written for: Basic and clinical neuroscientists, mass spectrometrists, protein scientists, bioinformaticians, neurologists, molecular and cellular biologists

Keywords:

Biofluid analysis
Bioinformatics
Biomarker research
Central nervous system - CNS
Clinical translation
Disease models
Mass spectrometry
Sub-proteome separations

Table of contents

1. The Methodology of Neuroproteomics
Andrew K. Ottens

Part I: Disease Models in Neuroproteomics

2. Modeling Cerebral Ischemia in Neuroproteomics
Jitendra R. Dave, Anthony J. Williams, Changping Yao, X-C. May Lu, and Frank C. Tortella

3. Clinical and Model Research of Neurotrauma
András Büki, Erzsebet Kovesdi, Jozsef Pal, and Endre Czeiter

4. Neuroproteomic Methods in Spinal Cord Injury
Anshu Chen and Joe E. Springer

5. Modeling Substance Abuse for Applications in Proteomics
Scott E. Hemby and Nilesh Tannu

6. Protein Aggregate Characterization in Models of Neurodegenerative Disease
Andrew T. N. Tebbenkamp and David R. Borchelt

Part II: Sub-Proteome Separations and Neuroproteomic Analysis

7. Sub-Proteome Processing: Isolation of Neuromelanin Granules from the Human Brain
Florian Tribl

8. Proteomic Analysis of Protein Phosphorylation and Ubiquitination in Alzheimer’s Disease
Stefani N. Thomas, Diane Cripps, and Austin J. Yang

9. Proteomics Identification of Carbonylated and HNE-Bound Brain Proteins in Alzheimer’s Disease
Rukhsana Sultana and D. Allan Butterfield

10. Mass Spectrometric Identification of in vivo Nitrotyrosine Sites in the Human Pituitary Tumor Proteome
Xianquan Zhan and Dominic M. Desiderio

11. Improved Enrichment and Proteomic Analysis of Brain Proteins with Signaling Function by Heparin Chromatography
Kurt Krapfenbauer and Michael Fountoulakis

12. Calmodulin Binding Proteome in the Brain
Zhiqun Zhang, Firas H. Kobeissy, Andrew K. Ottens, Juan A. Martínez, and Kevin K.W. Wang

Part III: Neuroproteomic Methodology and Bioinformatics

13. Separation of the Neuroproteome by Ion Exchange Chromatography
Brian F. Fuller and Andrew K. Ottens

14. iTRAQ-Based Shotgun Neuroproteomics
Tong Liu, Jun Hu, and Hong Li

15. Methods in Drug Abuse Neuroproteomics: Methamphetamine Psychoproteome
Firas H. Kobaissy, Zhiqun Zhang, Shankar Sadasivan, Mark S. Gold, and Kevin K.W. Wang

16. Shotgun Protein Identification and Quantification by Mass Spectrometry In Neuroproteomics
Bingwen Lu, Tao Xu, Robin Park, Daniel B. McClatchy, Lujian Liao, and John R. Yates III

Part IV: Biofluid Analysis and Clinical Translation

17. Identification of Glycoproteins in Human Cerebrospinal Fluid
Hye Jin Hwang, Thomas Quinn, and Jing Zhang

18. Mass Spectrometric Analysis of Body Fluids for Biomarker Discovery
David M. Good and Joshua J. Coon

19. Traumatic Brain Injury Biomarkers: From Pipeline to Diagnostic Assay Development
Monika W. Oli, Ronald L. Hayes, Gillian Robinson, and Kevin K.W. Wang

20. Translation of Neurological Biomarkers to Clinically Relevant Platforms
Ronald L. Hayes, Gillian Robinson, Uwe Muller, and Kevin K.W. Wang