Main description:

This volume focuses on protein analysis, including a wide range of the use of mass spectrometry and other protein methods within neurobiological disciplines. Chapters cover topics such as cerebrospinal fluid (CSF) processing and biobanking; label-free quantitative proteomics; SWATH; top-down proteomics; and experimental strategies based on other -omics applied to CSF metabolome, lipidome, and microRNAome. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and thorough, Cerebrospinal Fluid (CSF) Proteomics: Methods and Protocols is a valuable resource for graduate students and post-doctoral fellows interested in learning more about CSF proteotyping. It is also useful to established researchers seeking further insight into this growing field.

Contents:

Preface...Table of Contents...Contributing Authors...
Part I Introduction
1. The Human Brain Proteome Project: Biological and Technological ChallengesJoaquin Fernandez-Irigoyen, Fernando Corrales, and Enrique Santamaria
Part II Cerebrospinal Fluid Sample Preparation Methods for Proteomic Workflows
2. Guidelines for CSF Processing and Biobanking: Impact on the Identification and Development of Optimal CSF Protein BiomarkersYanaika S. Hok-a-Hin, Eline A. J. Willemse, Charlotte E. Teunissen, and Marta del Campo
3. Functional Analyses of Embryonic Cerebrospinal Fluid ProteinsTeresa Caprile, Francisco Lamus, Maria Isabel Alonso, Hernan Montecinos, and Angel Gato
4. CSF Sample Preparation for Data Independent AcquisitionKatalin Barkovits, Lars Toenges, and Katrin Marcus
5. Sample Fractionation Techniques for CSF Peptide Spectral Library GenerationSandra Pacharra, Katrin Marcus, and Caroline May
Part III Shotgun Cerebrospinal Fluid Proteomics
6. Application of 2D-DIGE and iTRAQ Workflows to Analyse CSF in Gliomas Aishwarya Rao, Kanika Mehta, Nikita Gahoi, and Sanjeeva Srivastava
7. Peptidomic Workflow Applied to Cerebrospinal Fluid AnalysisRustam H. Ziganshin, Sergey I. Kovalchuk, and Igor V. Azarkin
8. Quantitative Evaluation of Different Protein Fractions of Cerebrospinal Fluid using 18O Labeling Ramona Birke, Eberhard Krause, Michael Schumann, Ingolf E. Blasig, and Reiner F. Haseloff
9. A Versatile Workflow for Cerebrospinal Fluid Proteomic Analysis with Mass Spectrometry: A Matter of Choice between Deep Coverage and Sample ThroughputCharlotte Macron, Antonio Nunez Galindo, Ornella Cominetti, and Loic Dayon
10. Determination of Cerebrospinal Fluid Proteome Variations by Isobaric-Labeling Coupled to Strong Cation Exchange Chromatography and Tandem Mass-SpectrometryMercedes Lachen-Montes, Andrea Gonzalez-Morales, Joaquin Fernandez-Irigoyen, and Enrique Santamaria
11. SWATH Mass Spectrometry Applied to Cerebrospinal Fluid Differential Proteomics: Establishment of a Sample-Specific MethodSandra I. Anjo, Catia Santa, and Bruno Manadas
Part IV Cerebrospinal Fluid Subproteomics
12. Top-Down Proteomics Applied to Human CSFMarina Gay, Ester Sanchez-Jimenez, Laura Villarreal, Mar Vilanova, Romain Huguet, Gianluca Arauz-Garofalo, Mireia Diaz-Lobo, Daniel Lopez-Ferrer, and Marta Vilaseca
13. Application of an Aptamer-Based Proteomics Assay (SOMAscanTM) in Rat CSFAlba Simats, Laura Ramiro, Joan Montaner, and Teresa Garcia-Berrocoso
14. Monitoring the Cerebrospinal Fluid Cytokine Profile using Membrane-Based Antibody ArraysAndrea Gonzalez-Morales, Mercedes Lachen-Montes, Joaquin Fernandez-Irigoyen, and Enrique Santamaria
15. Selective and Sensitive Mass Spectrometric Identification of Immune Complexe Antigens in Cerebrospinal FluidNozomi Aibara and Kaname Ohyama
16. CSF N-glycoproteomics using MALDI MS Techniques in Neurodegenerative DiseasesAngela Messina, Angelo Palmigiano, Rosaria Ornella Bua, Donata Agata Romeo, Rita Barone, Luisa Sturiale, Mario Zappia, and Domenico Garozzo
17. Deployment of Label-Free Quantitative Olfactory Proteomics to Detect Cerebrospinal Fluid Biomarker Candidates in synucleinopathiesMercedes Lachen-Montes, Andrea Gonzalez-Morales, Joaquin Fernandez-Irigoyen, and Enrique Santamaria
18. An Improved Assay for Quantitation of Cerebrospinal Fluid Cystatin C using Liquid Chromatography Tandem Mass SpectrometryAbdullah Md Sheikh and Atsushi Nagai
19. Array-Based Profiling of Proteins and Autoantibody Repertoires in CSFElisa Pin, Ronald Sjoeberg, Eni Andersson, Cecilia Hellstroem, Jennie Olofsson, August Jernbom Falk, Sofia Bergstroem, Julia Remnestal, David Just, Peter Nilsson, and Anna Manberg
Part V Other -Omics Applied to Cerebrospinal Fluid
20. Untargeted Metabolomics Relative Quantification by SWATH Mass Spectrometry Applied to Cerebrospinal FluidVera M. Mendes, Margarida Coelho, and Bruno Manadas
21. Co-Extraction for Metabolomics and Proteomics from a Single CSF SamplePhilipp Hoermann, Katalin Barkovits, Katrin Marcus, and Karsten Hiller
22. Characterization of the Alzheimer's Disease MicroRNA Profile in Exosome Enriched CSF SamplesJavier Riancho, Ana Santurtun, and Pascual Sanchez-Juan
23. Mass-Spectrometry Applied to Human Cerebrospinal Fluid LipidomeLaura Millan, Joaquin Fernandez-Irigoyen, Enrique Santamaria, and Rebeca Mayo
Part VI Bioinformatics Applied to Cerebrospinal Fluid
24. Trait Loci Mapping and CSF ProteomeDaimei Sasayama, Kotaro Hattori, and Hiroshi Kunugi
25. Essential Features and Use Cases of the Cerebrospinal Fluid Proteome Resource (CSF-PR)Astrid Guldbrandsen, Yehia Farag, Ragnhild Reehorst Lereim, Frode S. Berven, and Harald Barsnes
26. Bioinformatics to Tackle the Biological Meaning of Human Cerebrospinal Fluid ProteomeFabio Trindade, Rita Nogueira-Ferreira, Paulo Bastos, Francisco Amado, Rita Ferreira, and Rui Vitorino