Neuroproteomics Methods and Protocols

Neuroproteomics: Methods and Protocols presents experimental details for applying proteomics to the study of the central nervous system (CNS) and its dysfunction through trauma and disease. The target audience includes clinical or basic scientists who look to apply proteomics to the neurosciences. Often researchers hear of proteomics without an adequate explanation of the methodology and inherent limitations. This volume conveys where proteomic methodology is in its application to CNS research and what results can be expected. We also address clinical translation of neuroproteomics, specifically in the area of biomarker research. The inception of neuroproteomics capitalized on rapid progress in large-molecule mass spectrometry over the last decade. Two seminal advances have spurred research – development of reliable polypeptide ionization processes and bioinformatics to rapidly process tandem mass spectra for peptide identification and quantification. What has followed is the exponential application of mass spectrometry to proteome characteri- tion across biological and biomedical disciplines. Arguably, the most elaborate proteomic implementation is in studying the CNS, the most enigmatic and complex animal system. Neuroscience is characterized by grandiose questions – what is consciousness, how does thought or memory work. Neuroproteomics researchers, however, have pri- rily involved themselves dysfunction, based on a pressing need (and invariably funding), in answering questions on CNS dysfunction, based on a pressing need (and invariably funding), and because such questions hold more accessible answers. Dysfunction is readily contrasted against normal function and presumably produces a lasting differential protein signature.

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 IonExchange 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