ArticleProceedings of the National Academy of Sciences of the United States of America2020
Sample multiplexing for targeted pathway proteomics in aging mice.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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73 citing papers in PubMed, 125 citations in OpenAlex.
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- Multiplexed Quantitation of Post-Translationally Modified Peptides in Single Cells Using Triggered MS/MS Combined with Super Heavy Tandem Mass Tags.Journal of proteome research · 2026Article
- Translational Remodeling of the Synaptic Proteome During Aging.Aging cell · 2025Article
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- Adipocyte FMO3-derived TMAO induces WAT dysfunction and metabolic disorders by promoting inflammasome activation in ageing.Nature communications · 2025Article
- Real-Time Instrument Control across Multiple Orbitrap Platforms through a Single Software Interface.Journal of proteome research · 2025Article
- Advancing biological understanding of cellular senescence with computational multiomics.Nature genetics · 2025Review
- A framework of biomarkers for adipose tissue aging: a consensus statement by the Aging Biomarker Consortium.Life medicine · 2025Article
- Current status and challenges of multi-omics research using animal models of atherosclerosis.Journal of molecular and cellular cardiology plus · 2025Review
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- Proteomic aging signatures across mouse organs and life stages.The EMBO journal · 2025Article
- Altered translation elongation contributes to key hallmarks of aging in the killifish brain.Science (New York, N.Y.) · 2025Article
- A longitudinal cohort study uncovers plasma protein biomarkers predating clinical onset and treatment response of rheumatoid arthritis.Nature communications · 2025Article
- Aging and diet alter the protein ubiquitylation landscape in the mouse brain.Nature communications · 2025Article
- Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells.Nature communications · 2025Article
13 more citing papers are in PubMed but not listed here.
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9 authors at 3 institutions in 1 country.
Funding
Abstract
Pathway proteomics strategies measure protein expression changes in specific cellular processes that carry out related functions. Using targeted tandem mass tags-based sample multiplexing, hundreds of proteins can be quantified across 10 or more samples simultaneously. To facilitate these highly complex experiments, we introduce a strategy that provides complete control over targeted sample multiplexing experiments, termed Tomahto, and present its implementation on the Orbitrap Tribrid mass spectrometer platform. Importantly, this software monitors via the external desktop computer to the data stream and inserts optimized MS2 and MS3 scans in real time based on an application programming interface with the mass spectrometer. Hundreds of proteins of interest from diverse biological samples can be targeted and accurately quantified in a sensitive and high-throughput fashion. It achieves sensitivity comparable to, if not better than, deep fractionation and requires minimal total sample input (∼10 µg). As a proof-of-principle experiment, we selected four pathways important in metabolism- and inflammation-related processes (260 proteins/520 peptides) and measured their abundance across 90 samples (nine tissues from five old and five young mice) to explore effects of aging. Tissue-specific aging is presented here and we highlight the role of inflammation- and metabolism-related processes in white adipose tissue. We validated our approach through comparison with a global proteome survey across the tissues, work that we also provide as a general resource for the community.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.