SMART 2.0 Statistical Metabolomics Analysis: An R Tool 2.0

Metabolomics has experienced significant growth and increased popularity due to technological advancements. We introduced an integrated tool for untargeted metabolomics analysis, SMART 1.0, that streamlined the entire analysis process, from initial data preprocessing to subsequent association analysis. With SMART 2.0, we enhanced SMART 1.0 by introducing new analytical modules in targeted metabolomics analysis, data normalization, quality control assessment, and advanced dimensionality reduction and classification methods. Additionally, SMART 2.0 offers integrative omics pathway analysis and postanalysis tasks such as peak identification and concentration calibration. We also explored the potential of using large language models for peak annotation and have found the results to be promising. This study employs narcotics data and breast cancer data as demonstrative examples to illustrate the new functionalities. The codes, a user guide, and example data can be downloaded at https://github.com/YuJenL/SMART.