Current Proteomic Approaches Applied to Brain Function

ISBN-13: 9781493971183 / Angielski / Twarda / 2017 / 360 str.

Enrique Santamaria; Joaquin Fernandez-Irigoyen

Opis

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.

Spis treści

Preface to the Series
Preface
Table of Contents
Contributing Authors

PART I Introduction

1. Brain Proteomics: Decoding Neuroproteomes using Mass-Spectrometry
Joaquín Fernández-Irigoyen and Enrique Santamaría 

PART II Labeling Methods in Neuroproteomics 

2. Applications of Amine-Reactive Tandem Mass Tags (TMT) in Human Neuroproteomics
Linnéa Lagerstedt, Leire Azurmendi, and Jean-Charles Sanchez

3. Application of Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) to Monitor Olfactory Proteomes during Alzheimer´s Disease Progression
Andrea González-Morales, Mercedes Lachén-Montes, María Ibañez-Vea, Enrique Santamaría, and Joaquín Fernández-Irigoyen 

4.  Protein Microarrays in Neurodegenerative Diseases
Pablo San Segundo-Acosta, María Garranzo-Asensio, Ana Montero-Calle, Carmen Oeo-Santos, Mayte Villalba, Ana Guzmán-Aránguez, 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 Naudí, Rosanna Cabré, Mariona Jové, and Reinald Pamplona

7. Methods for Human Olfactory Bulb-Tissue Studies using Peptide/Protein MALDI-TOF Imaging Mass Spectrometry (MALDI-IMS)
Ibon Iloro, Joaquín Fernández-Irigoyen, Iraide Escobes, Mikel Azkargorta, Enrique Santamaría, Felix Elortza

8. Neuroproteomics using Short GeLC-SWATH: From the Evaluation of Proteome Changes to the Clarification of Protein Function
Sandra I. Anjo, Cátia Santa, Susana C. Saraiva, Karolina Freitas, Faraj Barah, Bruno Carreira, Inês Araújo, 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 François Fenaille 

11. In Vivo Strategies to Isolate and Characterize the Neuronal Ubiquitinated Proteome
Juanma Ramírez, Nagore Elu, Aitor Martinez, Benoit Lectez, and Ugo Mayor

12. Characterization of the Phosphoproteome and Sialoproteome in Brain Tissues by Mass Spectrometry
María Ibañez-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 Alzheimer´s Disease using Oxidized Cysteine-Selective cPILOT
Ryan R. Dyer, Liqing Gu, and Renã A.S. Robinson 

PART V Subcellular Neuroproteomics

15. Proteomic Analysis of Extracellular Vesicles in Neurological Diseases
Matías Sáenz-Cuesta, Enrique Santamaría, Joaquín Fernández-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 Bayés

17. Nuclear Proteomics for Exploring MK-801 Treated Oligodendrocytes to Better Understand Schizophrenia
Aline G. Santana, Giuliana S. Zuccoli, Verônica 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