Cerebrospinal Fluid (Csf) Proteomics: Methods and Protocols

ISBN-13: 9781493997053 / Angielski / Twarda / 2019 / 557 str.

Enrique Santamaría; Joaquín Fernández-Irigoyen

Spis treści

Preface…

Table of Contents…

Contributing Authors…

Part I Introduction

1. The Human Brain Proteome Project: Biological and Technological Challenges

Joaquín Fernández-Irigoyen, Fernando Corrales, and Enrique Santamaría

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 Biomarkers

Yanaika S. Hok-a-Hin, Eline A. J. Willemse, Charlotte E. Teunissen, and Marta del Campo

3. Functional Analyses of Embryonic Cerebrospinal Fluid Proteins

Teresa Caprile, Francisco Lamus, María Isabel Alonso, Hernán Montecinos, and Angel Gato 

4.  CSF Sample Preparation for Data Independent Acquisition

Katalin Barkovits, Lars Tönges, and Katrin Marcus

5. Sample Fractionation Techniques for CSF Peptide Spectral Library Generation

Sandra 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 Analysis

Rustam 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 Schümann, 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 Throughput

Charlotte Macron, Antonio Núñez Galindo, Ornella Cominetti, and Loïc Dayon

10. Determination of Cerebrospinal Fluid Proteome Variations by Isobaric-Labeling Coupled to Strong Cation Exchange Chromatography and Tandem Mass-Spectrometry

Mercedes Lachén-Montes, Andrea González-Morales, Joaquín Fernández-Irigoyen, and Enrique Santamaría

11. SWATH Mass Spectrometry Applied to Cerebrospinal Fluid Differential Proteomics: Establishment of a Sample-Specific Method

Sandra I. Anjo, Cátia Santa, and Bruno Manadas

Part IV Cerebrospinal Fluid Subproteomics

12. Top-Down Proteomics Applied to Human CSF

Marina Gay, Ester Sánchez-Jiménez, Laura Villarreal, Mar Vilanova, Romain Huguet, Gianluca Arauz-Garofalo, Mireia Díaz-Lobo, Daniel López-Ferrer, and Marta Vilaseca

13. Application of an Aptamer-Based Proteomics Assay (SOMAscanTM) in Rat CSF

Alba Simats, Laura Ramiro, Joan Montaner, and Teresa García-Berrocoso

14. Monitoring the Cerebrospinal Fluid Cytokine Profile using Membrane-Based Antibody Arrays

Andrea González-Morales, Mercedes Lachén-Montes, Joaquín Fernández-Irigoyen, and Enrique Santamaría

15. Selective and Sensitive Mass Spectrometric Identification of Immune Complexe Antigens in Cerebrospinal Fluid

Nozomi Aibara and Kaname Ohyama

16. CSF N-glycoproteomics using MALDI MS Techniques in Neurodegenerative Diseases

Angela 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 synucleinopathies

Mercedes Lachén-Montes, Andrea González-Morales, Joaquín Fernández-Irigoyen, and 

Enrique Santamaría

18. An Improved Assay for Quantitation of Cerebrospinal Fluid Cystatin C using Liquid Chromatography Tandem Mass Spectrometry

Abdullah Md Sheikh and Atsushi Nagai

19. Array-Based Profiling of Proteins and Autoantibody Repertoires in CSF

Elisa Pin, Ronald Sjöberg, Eni Andersson, Cecilia Hellström, Jennie Olofsson, August Jernbom Falk, Sofia Bergström, Julia Remnestål, David Just, Peter Nilsson, and Anna Månberg

Part V Other –Omics Applied to Cerebrospinal Fluid

20. Untargeted Metabolomics Relative Quantification by SWATH Mass Spectrometry Applied to Cerebrospinal Fluid

Vera M. Mendes, Margarida Coelho, and Bruno Manadas

21. Co-Extraction for Metabolomics and Proteomics from a Single CSF Sample

Philipp Hörmann, Katalin Barkovits, Katrin Marcus, and Karsten Hiller

22. Characterization of the Alzheimer’s Disease MicroRNA Profile in Exosome Enriched CSF Samples

Javier Riancho, Ana Santurtun, and Pascual Sánchez-Juan

23. Mass-Spectrometry Applied to Human Cerebrospinal Fluid Lipidome

Laura Millán, Joaquín Fernández-Irigoyen, Enrique Santamaría, and Rebeca Mayo

Part VI Bioinformatics Applied to Cerebrospinal Fluid

24. Trait Loci Mapping and CSF Proteome

Daimei 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 Proteome

Fábio Trindade, Rita Nogueira-Ferreira, Paulo Bastos, Francisco Amado, Rita Ferreira, and Rui Vitorino   

Blurb

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.