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Data-Independent Acquisition Mass Spectrometry-Based Deep Proteome Analysis for Hydrophobic Proteins from Dried Blood Spots Enriched by Sodium Carbonate Precipitation

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Clinical Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2420))

Abstract

Dried blood spots (DBS) are widely used for screening molecular profiles, including enzymatic activity. However, hydrophilic proteins present in large amounts in blood inhibit detection of other proteins in DBS by liquid chromatography-mass spectrometry (LC-MS/MS) without preenrichment. Sodium carbonate precipitation (SCP) can concentrate hydrophobic proteins from DBS and effectively remove soluble hydrophilic proteins. Furthermore, SCP combination with data-independent acquisition (DIA) for quantitative LC-MS/MS enhanced the proteome analysis sensitivity and quantification limits. In this protocol, we have described in detail a simple preenrichment method using SCP and a deep proteome analysis method for LC-MS/MS data using DIA.

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Authors and Affiliations

  1. Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan

    Daisuke Nakajima, Osamu Ohara & Yusuke Kawashima

Authors
  1. Daisuke Nakajima
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  2. Osamu Ohara
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  3. Yusuke Kawashima
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Corresponding author

Correspondence to Yusuke Kawashima .

Editor information

Editors and Affiliations

  1. Proteomics Unit, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain

    Fernando J. Corrales

  2. Proteomics Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Madrid, Spain

    Alberto Paradela

  3. Proteomics Unit, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain

    Miguel Marcilla

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Nakajima, D., Ohara, O., Kawashima, Y. (2022). Data-Independent Acquisition Mass Spectrometry-Based Deep Proteome Analysis for Hydrophobic Proteins from Dried Blood Spots Enriched by Sodium Carbonate Precipitation. In: Corrales, F.J., Paradela, A., Marcilla, M. (eds) Clinical Proteomics. Methods in Molecular Biology, vol 2420. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1936-0_4

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  • DOI: https://doi.org/10.1007/978-1-0716-1936-0_4

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1935-3

  • Online ISBN: 978-1-0716-1936-0

  • eBook Packages: Springer Protocols

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