ArticleMolecular & cellular proteomics : MCP2012
Topograph, a software platform for precursor enrichment corrected global protein turnover measurements.
Article in Molecular & cellular proteomics : MCP, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Proteogenomic analysis of the differential stability of cardiac protein isoforms.bioRxiv : the preprint server for biology · 2026Article
- Kinetic control of macrophage death by PTM-turnover crosstalk in infection and inflammation.Cell chemical biology · 2026Review
- Nitric oxide required for transition to slower hepatic protein synthesis rates during long-term caloric restriction.The Journal of clinical investigation · 2026Article
- Mitochondrial DNA Instability Supersedes Parkin Mutations in Driving Mitochondrial Proteomic Alterations and Functional Deficits in Polg Mutator Mice.International journal of molecular sciences · 2024Article
- Identification and functional analysis of senescent cells in the cardiovascular system using omics approaches.American journal of physiology. Heart and circulatory physiology · 2023Review
- The transcription regulator ATF4 is a mediator of skeletal muscle aging.GeroScience · 2023Article
- Longitudinal in vivo metabolic labeling reveals tissue-specific mitochondrial proteome turnover rates and proteins selectively altered by parkin deficiency.Scientific reports · 2023Article
- Quantifying label enrichment from two mass isotopomers increases proteome coverage for in vivo protein turnover using heavy water metabolic labeling.Communications chemistry · 2023Article
- TurnoveR: A Skyline External Tool for Analysis of Protein Turnover in Metabolic Labeling Studies.Journal of proteome research · 2023Article
- Utilizing Nonequilibrium Isotope Enrichments to Dramatically Increase Turnover Measurement Ranges in Single Biopsy Samples from Humans.Journal of proteome research · 2022Article
- Protein lifetimes in aged brains reveal a proteostatic adaptation linking physiological aging to neurodegeneration.Science advances · 2022Article
- Protein turnover models for LC-MS data of heavy water metabolic labeling.Briefings in bioinformatics · 2022Article
- High-Resolution Mass Spectrometry for In Vivo Proteome Dynamics using Heavy Water Metabolic Labeling.International journal of molecular sciences · 2020Article
- Accumulation of "Old Proteins" and the Critical Need for MS-based Protein Turnover Measurements in Aging and Longevity.Proteomics · 2020Review
- Proteome Dynamics from Heavy Water Metabolic Labeling and Peptide Tandem Mass Spectrometry.International journal of mass spectrometry · 2019Article
- Autophagy accounts for approximately one-third of mitochondrial protein turnover and is protein selective.Autophagy · 2019Article
- Nitrogen sourcing during viral infection of marine cyanobacteria.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- 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.Journal of proteome research · 2018Article
- Article
- Glucocerebrosidase deficiency promotes protein aggregation through dysregulation of extracellular vesicles.PLoS genetics · 2018Article
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8 authors.
Funding
Abstract
Defects in protein turnover have been implicated in a broad range of diseases, but current proteomics methods of measuring protein turnover are limited by the software tools available. Conventional methods require indirect approaches to differentiate newly synthesized protein when synthesized from partially labeled precursor pools. To address this, we have developed Topograph, a software platform which calculates the fraction of peptides that are from newly synthesized proteins and their turnover rates. A unique feature of Topograph is the ability to calculate amino acid precursor pool enrichment levels which allows for accurate calculations when the precursor pool is not fully labeled, and the approach used by Topograph is applicable regardless of the stable isotope label used. We validate the Topograph algorithms using data acquired from a mouse labeling experiment and demonstrate the influence that precursor pool corrections can have on protein turnover measurements.
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