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Advances and Utility of the Human Plasma Proteome

Cite this: J. Proteome Res. 2021, 20, 12, 5241–5263
Publication Date (Web):October 21, 2021
https://doi.org/10.1021/acs.jproteome.1c00657
Copyright © 2021 American Chemical Society
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    Abstract

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    The study of proteins circulating in blood offers tremendous opportunities to diagnose, stratify, or possibly prevent diseases. With recent technological advances and the urgent need to understand the effects of COVID-19, the proteomic analysis of blood-derived serum and plasma has become even more important for studying human biology and pathophysiology. Here we provide views and perspectives about technological developments and possible clinical applications that use mass-spectrometry(MS)- or affinity-based methods. We discuss examples where plasma proteomics contributed valuable insights into SARS-CoV-2 infections, aging, and hemostasis and the opportunities offered by combining proteomics with genetic data. As a contribution to the Human Proteome Organization (HUPO) Human Plasma Proteome Project (HPPP), we present the Human Plasma PeptideAtlas build 2021-07 that comprises 4395 canonical and 1482 additional nonredundant human proteins detected in 240 MS-based experiments. In addition, we report the new Human Extracellular Vesicle PeptideAtlas 2021-06, which comprises five studies and 2757 canonical proteins detected in extracellular vesicles circulating in blood, of which 74% (2047) are in common with the plasma PeptideAtlas. Our overview summarizes the recent advances, impactful applications, and ongoing challenges for translating plasma proteomics into utility for precision medicine.

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jproteome.1c00657.

    • Supplementary Table S1. Union of proteins in both the plasma and blood extracellular vesicle PeptideAtlas builds, along with the crudely estimated log10 abundances and functional annotations (XLSX)

    • Supplementary Table S2. Top 10 most abundant proteins in the EV build without a detection in the plasma build. Additional information about the proteins and their RNA expression were derived for the Human Protein (XLSX)

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