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Omics Untargeted Key Script: R-Based Software Toolbox for Untargeted Metabolomics with Bladder Cancer Biomarkers Discovery Case Studyстатья
Статья опубликована в высокорейтинговом журнале
Информация о цитировании статьи получена из
Scopus
Статья опубликована в журнале из списка Web of Science и/или Scopus
Дата последнего поиска статьи во внешних источниках: 17 ноября 2021 г.
- Авторы: Plyushchenko Ivan V., Fedorova Elizaveta S., Potoldykova Natalia V., Polyakovskiy Konstantin A., Glukhov Alexander I., Rodin Igor A.
- Журнал: Journal of Proteome Research
- Год издания: 2021
- Издательство: American Chemical Society
- Местоположение издательства: United States
- Номер статьи: acs.jproteome.1c00392
- DOI: 10.1021/acs.jproteome.1c00392
- Аннотация: Large-scale untargeted LC-MS-based metabolomic profiling is a valuable source for systems biology and biomarker discovery. Data analysis and processing are major tasks due to the high complexity of generated signals and the presence of unwanted variations. In the present study, we introduce an R-based open-source collection of scripts called OUKS (Omics Untargeted Key Script), which provides comprehensive data processing. OUKS is developed by integrating various R packages and metabolomics software tools and can be easily set up and prepared to create a custom pipeline. Novel computational features are related to quality control samples-based signal processing and are implemented by gradient boosting, tree-based, and other nonlinear regression algorithms. Bladder cancer biomarkers discovery study which is based on untargeted LC-MS profiling of urine samples is performed to demonstrate exhaustive functionality of the developed software tool. Unique examination among dozens of metabolomics-specific data curation methods was carried out at each processing step. As a result, potential biomarkers were identified, statistically validated, and described by metabolism disorders. Our study demonstrates that OUKS helps to make untargeted LC-MS metabolomic profiling with the latest computational features readily accessible in a ready-to-use unified manner to a research community.
- Добавил в систему: Плющенко Иван Викторович