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Serum/Plasma Proteomics pp 103–117Cite as

Low-Molecular-Weight Plasma Proteome Analysis Using Top-Down Mass Spectrometry

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1619))

Abstract

While human plasma has a wealth of diagnostic information regarding the state of the human body in heath and disease, low molecular weight (LMW) proteome (<30 kDa) has been shown to contain a rich source of diagnostic biomarkers. Here we describe a protocol for top-down proteomic analysis to identify and characterize the LMW proteoforms present in four types of human plasma samples without immunoaffinity depletion and with depletion of the top two, six, and seven high-abundance proteins. Each type of plasma sample was first fractionated based on molecular weight using gel-eluted liquid fraction entrapment electrophoresis (GELFrEE). Then, the GELFrEE fractions containing up to 30 kDa were subjected to nanocapillary–LC–MS/MS, and the high-resolution MS and MS/MS data were processed using ProSightPC software. As a result, a total of 442 LMW proteins and cleaved products, including those with posttranslational modifications (PTMs) and single amino acid variations (SAAVs), were identified with a threshold E-value of 1 × 10−4 from the four types of plasma samples.

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Acknowledgments

The authors gratefully acknowledge the technical assistance from the Kelleher Group at Northwestern University. This work was supported by grants from the Multi-omics Program (2012M3A9B9036679) and the Brain Research Program (2015M3C7A1064795) funded through NRF supported by the Korean Ministry of Science, ICT and Future Planning and a KIST institutional program.

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Authors and Affiliations

  1. Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea

    Dong Huey Cheon, Eun Gyeong Yang, Cheolju Lee & Ji Eun Lee

  2. Interdisciplinary program of Integrated Biotechnology, Sogang University, Seoul, Republic of Korea

    Dong Huey Cheon

  3. Department of Biological Chemistry, University of Science and Technology, Daejeon, 305-333, Republic of Korea

    Cheolju Lee

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  1. Dong Huey Cheon
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  2. Eun Gyeong Yang
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  3. Cheolju Lee
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  4. Ji Eun Lee
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Corresponding author

Correspondence to Ji Eun Lee .

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Editors and Affiliations

  1. Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia

    David W. Greening

  2. Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia

    Richard J. Simpson

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Cheon, D.H., Yang, E.G., Lee, C., Lee, J.E. (2017). Low-Molecular-Weight Plasma Proteome Analysis Using Top-Down Mass Spectrometry. In: Greening, D., Simpson, R. (eds) Serum/Plasma Proteomics. Methods in Molecular Biology, vol 1619. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7057-5_8

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  • DOI: https://doi.org/10.1007/978-1-4939-7057-5_8

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7056-8

  • Online ISBN: 978-1-4939-7057-5

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