Description
This volume focuses on protein analysis covering a wide spectrum of the utility of mass spectrometry within neurobiological disciplines. The chapters in this book discuss label (iTRAQ, TMT, protein arrays) and label-free workflows (SWATH, MALDI Imaging, and label-free quantitation). Other chapters look at experimental strategies targeted to the identification and quantitation of specific lipids and post-translational modifications, as well as proteomic workflows that focus on characterization of subcellular proteomes. The last few chapters in the book describe various bioinformatics pipelines used to analyze the molecular data derived from high-throughput transcriptomic and proteomic experiments on brain tissue. The Neuromethods series offers chapters with key advice and procedure specifics to empower the readers to successfully achieve their own scientific and experimental goals. Thorough and comprehensive, Current Proteomic Approaches Applied to Brain Function is a valuable resource for graduate students and postdoctoral fellows interested in neuroproteomics, as well as researchers looking for further insight into the growing field of mass spectrometry in neuroscience. Preface to the Series Preface Table of Contents Contributing Authors PART I Introduction 1. Brain Proteomics: Decoding Neuroproteomes using Mass-Spectrometry Joaqun Fernndez-Irigoyen and Enrique Santamara PART II Labeling Methods in Neuroproteomics 2. Applications of Amine-Reactive Tandem Mass Tags (TMT) in Human Neuroproteomics Linna Lagerstedt, Leire Azurmendi, and Jean-Charles Sanchez 3. Application of Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) to Monitor Olfactory Proteomes during Alzheimers Disease Progression Andrea Gonzlez-Morales, Mercedes Lachn-Montes, Mara Ibaez-Vea, Enrique Santamara, and Joaqun Fernndez-Irigoyen 4. Protein Microarrays in Neurodegenerative Diseases Pablo San Segundo-Acosta, Mara Garranzo-Asensio, Ana Montero-Calle, Carmen Oeo-Santos, Mayte Villalba, Ana Guzmn-Arnguez, and Rodrigo Barderas PART III Label-Free Methods in Neuroproteomics 5. Comprehensive Shotgun Proteomic Analyses of Oligodendrocytes using Ion Mobility and Data Independent Acquisition Juliana S. Cassoli and Daniel Martins-de-Souza 6. Non-Targeted Brain Lipidomics Profiling Performed by UPLC-ESI-qTOF-MS/MS Alba Naud, Rosanna Cabr, Mariona Jov, and Reinald Pamplona 7. Methods for Human Olfactory Bulb-Tissue Studies using Peptide/Protein MALDI-TOF Imaging Mass Spectrometry (MALDI-IMS) Ibon Iloro, Joaqun Fernndez-Irigoyen, Iraide Escobes, Mikel Azkargorta, Enrique Santamara, Felix Elortza 8. Neuroproteomics using Short GeLC-SWATH: From the Evaluation of Proteome Changes to the Clarification of Protein Function Sandra I. Anjo, Ctia Santa, Susana C. Saraiva, Karolina Freitas, Faraj Barah, Bruno Carreira, Ins Arajo, and Bruno Manadas PART IV Mass Spectrometry-based Neuroproteomics to Analyze Post-Translational Modificiations 9. Analysis of Brain Phosphoproteome using Titanium Dioxide Enrichment and High Resolution LC-MS/MS Jeffrey M. Sifford, Haiyan Tan, Hong Wang, and Junmin Peng 10. N-Glycomics and N-Glycoproteomics of Human Cerebrospinal Fluid Sophie Cholet, Arnaud Goyallon, Christophe Junot, and Franois Fenaille 11. In Vivo Strategies to Isolate and Characterize the Neuronal Ubiquitinated Proteome Juanma Ramrez, Nagore Elu, Aitor Martinez, Benoit Lectez, and Ugo Mayor 12. Characterization of the Phosphoproteome and Sialoproteome in Brain Tissues by Mass Spectrometry Mara Ibaez-Vea, Stefan J. Kempf, and Martin R. Larsen 13. Proteomic Analysis of SUMOylation in the Post-Ischemic Brain J. Will Thompson, Meng Jiang, and Wei Yang 14. S-Nitrosylation in Alzheimers Disease using Oxidized Cysteine-Selective cPILOT Ryan R. Dyer, Liqing Gu, and Ren A.S. Robinson PART V Subcellular Neuroproteomics 15. Proteomic Analysis of Extracellular Vesicles in Neurological Diseases Matas Senz-Cuesta, Enrique Santamara, Joaqun Fernndez-Irigoyen, and David Otaegui 16. Quantitative In-Depth Profiling of the Postsynaptic Density Proteome to Understand the Molecular Mechanisms Governing Synaptic Physiology and Pathology Rita Reig-Viader and Alex Bays 17. Nuclear Proteomics for Exploring MK-801 Treated Oligodendrocytes to Better Understand Schizophrenia Aline G. Santana, Giuliana S. Zuccoli, Vernica Saia-Cereda, Juliana S. Cassoli, and Daniel Martins-de-Souza 18. Localized Proteomics of Individual Neurons Isolated from Formalin-Fixed, Paraffin Embedded Tissue Sections using Laser Capture Microdissection Eleanor Drummond, Shruti Nayak, Beatrix Ueberheide, and Thomas Wisniewski PART VI Bioinformatics 19. Creation of Reusable Bioinformatics Workflows for Reproducible Analysis of LC-MS Proteomics Data Julian Uskoreit, Maike Ahrens, Katalin Barkovits, Katrin Marcus, and Martin Eisencacher 20. Integration of Transcriptomic and Proteomic Data for Disease Insights Ravi Sirdeshmukh, Savita Jayaram, Manoj Kumar Gupta, Pranali Sonpatki, Manika Singh, Raksha A. Ganesh, Chaitra S. Reddy, and Nameeta Shah
