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High-Throughput Proteome Profiling of Plasma and Native Plasma Complexes Using Native Chromatography

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Serum/Plasma Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2628))

Abstract

We describe a high-throughput method for co-fractionation mass spectrometry (CF-MS) profiling for native plasma protein profiling. CF-MS allows the profiling of endogenous protein complexes between samples. Proteins often interact with other proteins and form macromolecular complexes that are different in disease states as well as cell states and cell types. This protocol describes an example for the sample preparation of 954 individual size exclusion chromatography (SEC) fractions, derived from 18 plasma samples that were separated into 53 fractions. Eighteen plasma samples were chosen based on the TMTpro multiplexing, but this methodology can be adapted for fewer or larger numbers of samples as appropriate. Our automated sample preparation method allows for high-throughput native plasma profiling, and we provide detailed methods for both a label-free and an isobaric labeling approach, discuss the merits of each approach, and detail the advantages of combining these strategies for comprehensive native plasma proteome profiling.

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Author information

Authors and Affiliations

  1. Calico Life Sciences LLC, South San Francisco, CA, USA

    Aleksandr Gaun, Niclas Olsson, John C. K. Wang, Dan L. Eaton & Fiona E. McAllister

Authors
  1. Aleksandr Gaun
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  2. Niclas Olsson
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  3. John C. K. Wang
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  4. Dan L. Eaton
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  5. Fiona E. McAllister
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Corresponding author

Correspondence to Fiona E. McAllister .

Editor information

Editors and Affiliations

  1. Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia

    David W. Greening

  2. Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, Melbourne, VIC, Australia

    Richard J. Simpson

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Gaun, A., Olsson, N., Wang, J.C.K., Eaton, D.L., McAllister, F.E. (2023). High-Throughput Proteome Profiling of Plasma and Native Plasma Complexes Using Native Chromatography. In: Greening, D.W., Simpson, R.J. (eds) Serum/Plasma Proteomics. Methods in Molecular Biology, vol 2628. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2978-9_5

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  • DOI: https://doi.org/10.1007/978-1-0716-2978-9_5

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2977-2

  • Online ISBN: 978-1-0716-2978-9

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