TidyMass an object-oriented reproducible analysis framework for LC–MS data

• DOI: 10.1038/s41467-022-32155-w
• Publication Date: 2022-07-28T05:02:50Z
• Authors: Xiaotao Shen; Hong Yan; Chuchu Wang; Peng Gao; Caroline H. Johnson; Michael P. Snyder
• Keywords: 0301 basic medicine; Science; Q; 0206 medical engineering; Reproducibility of Results; 02 engineering and technology; Article; Workflow; 03 medical and health sciences; Tandem Mass Spectrometry; Metabolomics; Ecosystem; Software; Chromatography, Liquid

AbstractReproducibility, traceability, and transparency have been long-standing issues for metabolomics data analysis. Multiple tools have been developed, but limitations still exist. Here, we present the tidyMass project (https://www.tidymass.org/), a comprehensive R-based computational framework that can achieve the traceable, shareable, and reproducible workflow needs of data processing and analysis for LC-MS-based untargeted metabolomics. TidyMass is an ecosystem of R packages that share an underlying design philosophy, grammar, and data structure, which provides a comprehensive, reproducible, and object-oriented computational framework. The modular architecture makes tidyMass a highly flexible and extensible tool, which other users can improve and integrate with other tools to customize their own pipeline.