PreprintCited by 15Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsMetabolomics and Mass Spectrometry Studies

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Spatial top-down proteomics for the functional characterization of human kidney

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Preprint — published as 10.1186/s12014-025-09531-x

Abstract

Background: The Human Proteome Project has credibly detected nearly 93% of the roughly 20,000 proteins which are predicted by the human genome. However, the proteome is enigmatic, where alterations in amino acid sequences from polymorphisms and alternative splicing, errors in translation, and post-translational modifications result in a proteome depth estimated at several million unique proteoforms. Recently mass spectrometry has been demonstrated in several landmark efforts mapping the human proteoform landscape in bulk analyses. Herein, we developed an integrated workflow for characterizing proteoforms from human tissue in a spatially resolved manner by coupling laser capture microdissection, nanoliter-scale sample preparation, and mass spectrometry imaging. Results: Using healthy human kidney sections as the case study, we focused our analyses on the major functional tissue units including glomeruli, tubules, and medullary rays. After laser capture microdissection, these isolated functional tissue units were processed with microPOTS (microdroplet processing in one-pot for trace samples) for sensitive top-down proteomics measurement. This provided a quantitative database of 616 proteoforms that was further leveraged as a library for mass spectrometry imaging with near-cellular spatial resolution over the entire section. Notably, several mitochondrial proteoforms were found to be differentially abundant between glomeruli and convoluted tubules, and further spatial contextualization was provided by mass spectrometry imaging confirming unique differences identified by microPOTS, and further expanding the field-of-view for unique distributions such as enhanced abundance of a truncated form (1-74) of ubiquitin within cortical regions. Conclusions: We developed an integrated workflow to directly identify proteoforms and reveal their spatial distributions. Where of the 20 differentially abundant proteoforms identified as discriminate between tubules and glomeruli by microPOTS, the vast majority of tubular proteoforms were of mitochondrial origin (8 of 10) where discriminate proteoforms in glomeruli were primarily hemoglobin subunits (9 of 10). These trends were also identified within ion images demonstrating spatially resolved characterization of proteoforms that has the potential to reshape discovery-based proteomics because the proteoforms are the ultimate effector of cellular functions. Applications of this technology have the potential to unravel etiology and pathophysiology of disease states, informing on biologically active proteoforms, which remodel the proteomic landscape in chronic and acute disorders.

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Metadata

Authors
Zemaitis, K. J., Fulcher, J. M., Kumar, R., Degnan, D. J., Lewis, L. A., Liao, Y.-C., Veličković, M., Williams, S. M., Moore, R. J., Bramer, L. M., Veličković, D., Zhu, Y., Zhou, M., & Paša-Tolić, L.
Affiliations
Pacific Northwest National Laboratory (US)
Venue
Clinical Proteomics
Publisher
openRxiv
Published
2024-02-13
Volume
22
Issue
1
Pages
9-9
ISSN
1542-6416 (ISSN-L)
OpenAlex
W4408216616
Cited by
15
References
1
Citations by year
2026: 9 · 2025: 4 · 2024: 2
FWCI
3.27
Type
journal article
Language
en
Open access
Licence
cc-by-nc-nd
Locations
  • Clinical Proteomics (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
  • PubMed Central (submittedVersion, cc-by-nc-nd)
Funders
  • U.S. Department of Energy (DE-AC05–76RL01830, 76RL01830, AC05-76RL01830, DE-AC05?)
  • Vanderbilt University
  • Northwestern University
  • National Institutes of Health (DE-AC05-76RL01830)
  • Office of Science (DE‐AC05‐76 RL01830)
  • National Cancer Institute (UH3CA256959, UG3CA256959)
  • Biological and Environmental Research (DE-AC05-76 RL01830, AC05-76RL01830, 76RL01830)
  • Pacific Northwest National Laboratory (DEAC0576RL01830, 76RL01830)
  • Common Fund
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
Keywords
proteoforms, human kidney, top-down proteomics, spatial proteomics, mass spectrometry imaging, laser capture microdissection, glomeruli, renal tubules, medullary rays, hemoglobin subunits

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