ArticleJournal of proteome research2018
d2ome, Software for in Vivo Protein Turnover Analysis Using Heavy Water Labeling and LC-MS, Reveals Alterations of Hepatic Proteome Dynamics in a Mouse Model of NAFLD.
Article in Journal of proteome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 39 papers.
What it found
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Who cites it
39 citing papers in PubMed.
- Kinetic Lipidomics: QuantifyingbioRxiv : the preprint server for biology · 2026Article
- A Computational Model for Determining Labeling Duration in Protein Turnover Studies Using a Single Deuterated Water Labeled Sample.Journal of the American Society for Mass Spectrometry · 2026Article
- Resilience of the mitochondrial reticulum in aging.American journal of physiology. Endocrinology and metabolism · 2025Article
- Deuterium labeling enables proteome-wide turnover kinetics analysis in cell culture.Cell reports methods · 2025Article
- Chronic Alcohol Consumption Reprograms Hepatic Metabolism Through Organelle-Specific Acetylation in Mice.Molecular & cellular proteomics : MCP · 2025Article
- Proteostatic Imbalance Drives the Pathogenesis and Age-Related Exacerbation of Heart Failure With Preserved Ejection Fraction.JACC. Basic to translational science · 2025Article
- Metformin treatment results in distinctive skeletal muscle mitochondrial remodeling in rats with different intrinsic aerobic capacities.Aging cell · 2024Article
- Numbers of Exchangeable Hydrogens from LC-MS Data of Heavy Water Metabolically Labeled Samples.Journal of the American Society for Mass Spectrometry · 2024Article
- Enabling population protein dynamics through Bayesian modeling.Bioinformatics (Oxford, England) · 2024Article
- Metabolomic and proteomic applications to exercise biomedicine.Translational exercise biomedicine · 2024Review
- Flexible Quality Control for Protein Turnover Rates Using d2ome.International journal of molecular sciences · 2023Article
- Impaired proteostatic mechanisms other than decreased protein synthesis limit old skeletal muscle recovery after disuse atrophy.Journal of cachexia, sarcopenia and muscle · 2023Article
- A large-scale LC-MS dataset of murine liver proteome from time course of heavy water metabolic labeling.Scientific data · 2023Article
- Kinetic proteomics identifies targeted changes in liver metabolism and the ribo-interactome by dietary sulfur amino acid restriction.GeroScience · 2023Article
- Skeletal and cardiac muscle have different protein turnover responses in a model of right heart failure.GeroScience · 2023Article
- A high-fat diet increases hepatic mitochondrial turnover through restricted acetylation in a NAFLD mouse model.American journal of physiology. Endocrinology and metabolism · 2023Article
- Quantifying label enrichment from two mass isotopomers increases proteome coverage for in vivo protein turnover using heavy water metabolic labeling.Communications chemistry · 2023Article
- Conditional Fragment Ion Probabilities Improve Database Searching for Nonmonoisotopic Precursors.Journal of proteome research · 2023Article
- Retention Time Alignment for Protein Turnover Studies Using Heavy Water Metabolic Labeling.Journal of proteome research · 2023Article
- TurnoveR: A Skyline External Tool for Analysis of Protein Turnover in Metabolic Labeling Studies.Journal of proteome research · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
Abstract
Metabolic labeling with heavy water followed by LC-MS is a high throughput approach to study proteostasis in vivo. Advances in mass spectrometry and sample processing have allowed consistent detection of thousands of proteins at multiple time points. However, freely available automated bioinformatics tools to analyze and extract protein decay rate constants are lacking. Here, we describe d2ome-a robust, automated software solution for in vivo protein turnover analysis. d2ome is highly scalable, uses innovative approaches to nonlinear fitting, implements Grubbs' outlier detection and removal, uses weighted-averaging of replicates, applies a data dependent elution time windowing, and uses mass accuracy in peak detection. Here, we discuss the application of d2ome in a comparative study of protein turnover in the livers of normal vs Western diet-fed LDLR
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Registered trials
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.