This new edition provides updated and novel protocols of neuroproteomics methods that encompass both global-scale as well as targeted and specialized topics, which are timely additions for the molecular and phenotypic analysis of the central nervous system and CNS-related disorders. The detailed contents of this book include the exploration of several exciting areas of advanced methods used for neuroproteomics research including relative and absolute protein quantitation by mass spectrometry, characterization of post-translational modifications, as well as bioinformatics and computational approaches. Written for the highly successful Methods in Molecular Biology series, methodology chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.
Part I: Current Reviews of Neuroproteomics Approaches and Applications
1. Neuroproteomics Studies: Challenges and Updates
Naify Ramadan, Hussein Gazalah, Mohammad El-Sayyad, Mohamad El-Haress, and Firas H. Kobeissy
2. Progress and Potential of Imaging Mass Spectrometry Applied to Biomarker Discovery
Jusal Quanico, Julien Franck, Maxence Wisztorski, Michel Salzet, and Isabelle Fournier
3. Biofluid Proteomics and Biomarkers in Traumatic Brain Injury
Safa Azar, Anwarul Hasan, Richard Younes, Farah Najdi, Lama Baki, Hussein Gazalah, Firas H. Kobeissy, Kazem Zibara, and Stefania Mondello
4. Degradomics in Neurotrauma: Profiling Traumatic Brain Injury
Hadi Abou-El-Hassan, Fares Sukhon, Edwyn Assaf, Hisham Bahmad, Hussein Abou-Abbass, Hussam Jourdi, and Firas H. Kobeissy
5. Evolving Relevance of Neuroproteomics in Alzheimer’s Disease
Simone Lista, Henrik Zetterberg, Sid E. O’Bryant, Kaj Blennow, and Harald Hampel
6. Genome to Phenome: A Systems Biology Approach to PTSD Using an Animal Model
Nabarun Chakraborty, James Meyerhoff, Marti Jett, and Rasha Hammamieh
Part II: Experimental Methods
7. Photoaffinity Labeling of Pentameric Ligand-Gated Ion Channels to Identify: A Proteomic Approach to Identify Allosteric Ligand Binding Sites
Selwyn S. Jayakar, Gordon Ang, David C. Chiara, and Ayman K. Hamouda
8. Quantitative Phosphoproteomic Analysis of Brain Tissues
Bing Bai, Haiyan Tan, and Junmin Peng
9. Glycoproteins Enrichment and LC-MS/MS Glycoproteomics in Central Nervous System Applications
Rui Zhu, Ehwang Song, Ahmed Hussein, Firas H. Kobeissy, and Yehia Mechref
10. A Novel 2-DE-Based Proteomic Analysis to Identify Multiple Substrates for Specific Protease in Neuronal Cells
Chiho Kim and Young J. Oh
11. Neuroproteomic Profiling of Cerebrospinal Fluid (CSF) by Multiplexed Affinity Arrays
Anna Häggmark, Peter Nilsson, and Jochen M. Schwenk
12. Isolation and Proteomic Analysis of Microvesicles and Exosomes from HT22 Cells and Primary Neurons
Richard Witas, Dale Chaput, Hirah Khan, Stanley M. Stevens, Jr., and David Kang
13. Combined MALDI Mass Spectrometry Imaging and Parafilm-Assisted Microdissection-Based LC-MS/MS Workflows in the Study of the Brain
Jusal Quanico, Julien Franck, Maxence Wisztorski, Michel Salzet, and Isabelle Fournier
14. De Novo and Uninterrupted SILAC Labeling of Primary Microglia
Ping Zhang, Ashley Culver-Cochran, Stanley M. Stevens, Jr., and Bin Liu
15. Spike-In SILAC Approach for Proteomic Analysis of Ex Vivo Microglia
Joao Paulo Costa Pinho, Harris Bell-Temin, Bin Liu, and Stanley M. Stevens, Jr.
16. A Proteomic Evaluation of Sympathetic Activity Biomarkers of the Hypothalamus-Pituitary-Adrenal Axis by Western Blotting Technique Following Experimental Traumatic Brain Injury
Hale Zerrin Toklu, Yasemin Sakarya, and Nihal Tümer
Part III: Bioinformatic and Computational Methods
17. Efficient and Accurate Algorithm for Cleaved Fragments Prediction (CFPA)
in Protein Sequences Dataset Based on Consensus and Its Variants: A Novel Degradomics Prediction Application
Atlal El-Assaad, Zaher Dawy, Georges Nemer, Hazem Hajj, and Firas H. Kobeissy
18. Effect of Second-Hand Tobacco Smoke on the Nitration of Brain Proteins: A Systems Biology & Bioinformatics Approach
Firas H. Kobeissy, Joy Guingab-Cagmat, Adriaan W. Bruijnzeel, Mark S. Gold, and Kevin Wang
19. An Advanced Omic Approach to Identify Co-Regulated Clusters and Transcription Regulation Network with AGCT and SHOE Methods
Natalia Polouliakh and Richard Nock
20. AutoDock and AutoDockTools for Protein-Ligand Docking: Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1(BACE1) as a Case Study
Nehme El-Hachem, Benjamin Haibe-Kains, Athar Khalil, Firas H. Kobeissy, and Georges Nemer
21. An Integration of Decision Tree and Visual Analysis to Analyze Intracranial Pressure
Soo-Yeon Ji, Kayvan Najarian, Toan Huyn, and Dong Hyun Jeong
This new edition provides updated and novel protocols of neuroproteomics methods that encompass both global-scale as well as targeted and specialized topics, which are timely additions for the molecular and phenotypic analysis of the central nervous system and CNS-related disorders. The detailed contents of this book include the exploration of several exciting areas of advanced methods used for neuroproteomics research including relative and absolute protein quantitation by mass spectrometry, characterization of post-translational modifications, as well as bioinformatics and computational approaches. Written for the highly successful Methods in Molecular Biology series, methodology chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.
Includes fully updated cutting-edge techniques for the study of neuroproteomics
