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Top-Down Proteomics Applied to Human Cerebrospinal Fluid

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Book cover Cerebrospinal Fluid (CSF) Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2044))

Abstract

Cerebrospinal fluid (CSF) is the fluid of choice to study pathologies and disorders of the central nervous system (CNS). Its composition, especially its proteins and peptides, holds the promise that it may reflect the pathological state of an individual. Traditionally, proteins and peptides in CSF have been analyzed using bottom-up proteomics technologies in the search of high proteome coverage. However, the limited protein sequence coverage of this technology means that information regarding post-translational modifications (PTMs) and alternative splice variants is lost. As an alternative technology, top-down proteomics offers low to medium proteome coverage, but high protein coverage enabling almost a full characterization of the proteins’ primary structure. This allows us to precisely identify distinct molecular forms of proteins (proteoforms) as well as naturally occurring bioactive peptide fragments, which could be of critical biological relevance and would otherwise remain undetected with a classical proteomics approach.

Here, we describe various strategies including sample preparation protocols, off-line intact protein prefractionation, and LC-MS/MS methods together with data analysis pipelines to analyze cerebrospinal fluid (CSF) by top-down proteomics. However, there is not a unique or standardized method and the selection of the top-down strategy will depend on the exact goal of the study. Here, we describe various top-down proteomics methods that enable rapid protein characterization and may be an excellent companion analytical workflow in the search for new protein biomarkers in neurodegenerative diseases.

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Acknowledgements

The authors thank Argyro Dermitzaki for the help in bibliographic search and Antonio Lorenzo for their assistance. They also thank Thermo Scientific for their support, Prof. Jacques Borg, formerly at Université Jean Monnet, Saint-Étienne, France, for his transfer of knowledge about CSF, and Prof. Neil Kelleher and Dr. Ken Durbin from Northwestern University for the data analysis tools and support.

This work was supported by IRB Barcelona funds. The IRB Barcelona Mass Spectrometry and Proteomics Core Facility, where most of the CSF analyses have been performed, has been active part of the BMBS European COST Action BM 1403 and is a member of Proteored, PRB3-ISCIII, supported by grant PRB3 (PT17/0019/0022- ISCIII-SGEFI / ERDF).

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Authors and Affiliations

  1. Mass Spectrometry and Proteomics Core Facility, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain

    Marina Gay, Ester Sánchez-Jiménez, Laura Villarreal, Mar Vilanova, Gianluca Arauz-Garofalo, Mireia Díaz-Lobo & Marta Vilaseca

  2. Thermo Fisher Scientific, San Jose, CA, USA

    Romain Huguet & Daniel López-Ferrer

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  1. Marina Gay
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  2. Ester Sánchez-Jiménez
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  3. Laura Villarreal
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  4. Mar Vilanova
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  6. Gianluca Arauz-Garofalo
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  9. Marta Vilaseca
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Correspondence to Marta Vilaseca .

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Editors and Affiliations

  1. Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain

    Enrique Santamaría

  2. Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain

    Joaquín Fernández-Irigoyen

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Gay, M. et al. (2019). Top-Down Proteomics Applied to Human Cerebrospinal Fluid. In: Santamaría, E., Fernández-Irigoyen, J. (eds) Cerebrospinal Fluid (CSF) Proteomics. Methods in Molecular Biology, vol 2044. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9706-0_12

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  • DOI: https://doi.org/10.1007/978-1-4939-9706-0_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9705-3

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