Expanding the landscape of aging via orbitrap astral mass spectrometry and tandem mass tag integration
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...
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Nature Portfolio
2025-05-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-60022-x |
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| author | 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 Tian Zhang |
| author_facet | 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 Tian Zhang |
| author_sort | Gregory R. Keele |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-b07d8afc908c4e02bab1dacc151917e5 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-b07d8afc908c4e02bab1dacc151917e52025-08-20T03:46:12ZengNature PortfolioNature Communications2041-17232025-05-0116111510.1038/s41467-025-60022-xExpanding the landscape of aging via orbitrap astral mass spectrometry and tandem mass tag integrationGregory R. Keele0Yue Dou1Seth P. Kodikara2Erin D. Jeffery3Dina L. Bai4Erik Hultenius5Zichen Gao6Joao A. Paulo7Steven P. Gygi8Xiao Tian9Tian Zhang10GenOmics, Bioinformatics, and Translational Research Center, RTI InternationalDepartment of Biochemistry and Molecular Genetics, School of Medicine, University of VirginiaDepartment of Biochemistry and Molecular Genetics, School of Medicine, University of VirginiaDepartment of Biochemistry and Molecular Genetics, School of Medicine, University of VirginiaDepartment of Biochemistry and Molecular Genetics, School of Medicine, University of VirginiaSanford Burnham Prebys Medical Discovery InstituteSanford Burnham Prebys Medical Discovery InstituteDepartment of Cell Biology, Harvard Medical SchoolDepartment of Cell Biology, Harvard Medical SchoolSanford Burnham Prebys Medical Discovery InstituteDepartment of Biochemistry and Molecular Genetics, School of Medicine, University of VirginiaAbstract 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.https://doi.org/10.1038/s41467-025-60022-x |
| spellingShingle | 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 Tian Zhang Expanding the landscape of aging via orbitrap astral mass spectrometry and tandem mass tag integration Nature Communications |
| title | Expanding the landscape of aging via orbitrap astral mass spectrometry and tandem mass tag integration |
| title_full | Expanding the landscape of aging via orbitrap astral mass spectrometry and tandem mass tag integration |
| title_fullStr | Expanding the landscape of aging via orbitrap astral mass spectrometry and tandem mass tag integration |
| title_full_unstemmed | Expanding the landscape of aging via orbitrap astral mass spectrometry and tandem mass tag integration |
| title_short | Expanding the landscape of aging via orbitrap astral mass spectrometry and tandem mass tag integration |
| title_sort | expanding the landscape of aging via orbitrap astral mass spectrometry and tandem mass tag integration |
| url | https://doi.org/10.1038/s41467-025-60022-x |
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