JUMPt: Comprehensive Protein Turnover Modeling of In Vivo Pulse SILAC Data by Ordinary Differential Equations
| العنوان: | JUMPt: Comprehensive Protein Turnover Modeling of In Vivo Pulse SILAC Data by Ordinary Differential Equations |
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| المؤلفون: | Xueyan Liu, Yuxin Li, Ji-Hoon Cho, Surendhar Reddy Chepyala, Junmin Peng, Yun Jiao, Ariana Mancieri, Zhiping Wu, Hui Zhang, Alex M. Breuer, Ka Yang |
| المصدر: | Anal Chem |
| بيانات النشر: | American Chemical Society (ACS), 2021. |
| سنة النشر: | 2021 |
| مصطلحات موضوعية: | Proteomics, chemistry.chemical_classification, Proteome, Chemistry, Protein turnover, Ode, Computational biology, Protein degradation, Mass Spectrometry, Article, Analytical Chemistry, Amino acid, Mice, In vivo, Isotope Labeling, Stable isotope labeling by amino acids in cell culture, Proteolysis, Animals |
| الوصف: | Recent advances in mass spectrometry (MS)-based proteomics allow the measurement of turnover rates of thousands of proteins using dynamic labeling methods, such as pulse stable isotope labeling by amino acids in cell culture (pSILAC). However, when applying the pSILAC strategy to multicellular animals (e.g., mice), the labeling process is significantly delayed by native amino acids recycled from protein degradation in vivo, raising a challenge of defining accurate protein turnover rates. Here, we report JUMPt, a software package using a novel ordinary differential equation (ODE)-based mathematical model to determine reliable rates of protein degradation. The uniqueness of JUMPt is to consider amino acid recycling and fit the kinetics of the labeling amino acid (e.g., Lys) and whole proteome simultaneously to derive half-lives of individual proteins. Multiple settings in the software are designed to enable simple to comprehensive data inputs for precise analysis of half-lives with flexibility. We examined the software by studying the turnover of thousands of proteins in the pSILAC brain and liver tissues. The results were largely consistent with the proteome turnover measurements from previous studies. The long-lived proteins are enriched in the integral membrane, myelin sheath, and mitochondrion in the brain. In summary, the ODE-based JUMPt software is an effective proteomics tool for analyzing large-scale protein turnover, and the software is publicly available on GitHub (https://github.com/JUMPSuite/JUMPt) to the research community. |
| تدمد: | 1520-6882 0003-2700 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::85d0fd6503c33d60016938a1dd909d19 https://doi.org/10.1021/acs.analchem.1c02309 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....85d0fd6503c33d60016938a1dd909d19 |
| قاعدة البيانات: | OpenAIRE |
Find this issue from the American Chemical Society | تدمد: | 15206882 00032700 |
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