Miso: an R package for multiple isotope labeling assisted metabolomics data analysis

Abstract

Abstract Motivation The use of stable isotope labeling is highly advantageous for structure elucidation in metabolomics studies. However, computational tools dealing with multiple-precursor-based labeling studies are still missing. Hence, we developed Miso, an R package providing automated and efficient data analysis workflow to detect the complete repertoire of labeled molecules from multiple-precursor-based labeling experiments. Results The capability of Miso is demonstrated by the analysis of liquid chromatography-mass spectrometry data obtained from duckweed plants fed with one unlabeled and two differently labeled tyrosine (unlabeled tyrosine, tyrosine-2H4 and tyrosine-13C915N1). The resulting data matrix generated by Miso contains sets of unlabeled and labeled ions with their retention time, m/z values and number of labeled atoms that can be directly utilized for database query and biological studies. Availability and implementation Miso is publicly available on the CRAN repository (https://cran.r-project.org/web/packages/Miso). A reproducible case study and a detailed tutorial are available from GitHub (https://github.com/YonghuiDong/Miso_example). Supplementary information Supplementary data are available at Bioinformatics online.