Expanding the landscape of aging via orbitrap astral mass spectrometry and tandem mass tag integration

Gregory R. Keele, Yue Dou, Seth P. Kodikara, Erin D. Jeffery, Dina L. Bai, Erik Hultenius, Zichen Gao, Joao A. Paulo, Steven P. Gygi, Xiao Tian and Tian Zhang ()
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Gregory R. Keele: RTI International
Yue Dou: University of Virginia
Seth P. Kodikara: University of Virginia
Erin D. Jeffery: University of Virginia
Dina L. Bai: University of Virginia
Erik Hultenius: Harvard Medical School
Zichen Gao: Harvard Medical School
Joao A. Paulo: Sanford Burnham Prebys Medical Discovery Institute
Steven P. Gygi: Sanford Burnham Prebys Medical Discovery Institute
Xiao Tian: Harvard Medical School
Tian Zhang: University of Virginia

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract Aging results in a progressive decline in physiological function due to the deterioration of essential biological processes. While proteomics offers insights into aging mechanisms, prior studies are limited in proteome coverage and lifespan range. To address this, we integrate the Orbitrap Astral Mass Spectrometer with the multiplex tandem mass tag (TMT) technology to profile the proteomes of cortex, hippocampus, striatum and kidney in the C57BL/6JN mice, quantifying 8,954 to 9,376 proteins per tissue (12,749 total). Samples spanned both sexes and three age groups (3, 12, and 20 months), representing early to late adulthood. To improve TMT quantitation accuracy, we develop a peptide-spectrum match-based filtering strategy that leverages resolution and signal-to-noise thresholds. Our analysis uncovers distinct tissue-specific patterns of protein abundance, with age and sex differences in the kidney and primarily age-related changes in brain tissues. We also identify both linear and non-linear proteomic trajectories with age, revealing complex protein dynamics over the adult lifespan. Integrating our findings with early developmental proteomic data from brain tissues highlights further divergent age-related trajectories, particularly in synaptic proteins. This study provides a robust data analysis workflow for Orbitrap Astral–based TMT analysis and expands the proteomic understanding of aging across tissues, ages, and sexes.

Date: 2025
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DOI: 10.1038/s41467-025-60022-x

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