Preface to the Series
Preface
Table of Contents
Contributing Authors
PART I Introduction
1. Brain Proteomics: Decoding Neuroproteomes using Mass-Spectrometry
Joaquin Fernandez-Irigoyen and Enrique Santamaria
PART II Labeling Methods in Neuroproteomics
2. Applications of Amine-Reactive Tandem Mass Tags (TMT) in Human Neuroproteomics
Linnea 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 Gonzalez-Morales, Mercedes Lachen-Montes, Maria Ibanez-Vea, Enrique Santamaria, and Joaquin Fernandez-Irigoyen
4. Protein Microarrays in Neurodegenerative Diseases
Pablo San Segundo-Acosta, Maria Garranzo-Asensio, Ana Montero-Calle, Carmen Oeo-Santos, Mayte Villalba, Ana Guzman-Aranguez, 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 Naudi, Rosanna Cabre, Mariona Jove, and Reinald Pamplona
7. Methods for Human Olfactory Bulb-Tissue Studies using Peptide/Protein MALDI-TOF Imaging Mass Spectrometry (MALDI-IMS)
Ibon Iloro, Joaquin Fernandez-Irigoyen, Iraide Escobes, Mikel Azkargorta, Enrique Santamaria, Felix Elortza
8. Neuroproteomics using Short GeLC-SWATH: From the Evaluation of Proteome Changes to the Clarification of Protein Function
Sandra I. Anjo, Catia Santa, Susana C. Saraiva, Karolina Freitas, Faraj Barah, Bruno Carreira, Ines Araujo, 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 Francois Fenaille
11. In Vivo Strategies to Isolate and Characterize the Neuronal Ubiquitinated Proteome
Juanma Ramirez, Nagore Elu, Aitor Martinez, Benoit Lectez, and Ugo Mayor
12. Characterization of the Phosphoproteome and Sialoproteome in Brain Tissues by Mass Spectrometry
Maria Ibanez-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 Rena A.S. Robinson
PART V Subcellular Neuroproteomics
15. Proteomic Analysis of Extracellular Vesicles in Neurological Diseases
Matias Saenz-Cuesta, Enrique Santamaria, Joaquin Fernandez-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 Bayes
17. Nuclear Proteomics for Exploring MK-801 Treated Oligodendrocytes to Better Understand Schizophrenia
Aline G. Santana, Giuliana S. Zuccoli, Veronica 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