MMEASE: enhanced analytical workflow for single-cell metabolomics

Metabolomics is essential for providing an overview of what chemical processes are taking place. A clear shift from bulk metabolomics to single-cell metabolomics (SCM) is observed in current research, and an integral workflow enabling the analysis of SCM data is therefore in great demand. However, no such workflow has been available to date. Herein, MMEASE, previously designed for analyzing bulk metabolomic data, was therefore updated to its 2.0 version by developing the first comprehensive and in-depth workflow analyzing SCM data. First, it provided all sequential steps of modern SCM research (from SCM data processing, to cellular heterogeneity analysis, then to high-resolution metabolite annotation, and finally to cell-based biological interpretation). Second, compared with the existing tools, MMEASE 2.0 was superior by incorporating the widest variety of methods at every step of the SCM analyses. The originality and functionality of our MMEASE were extensively validated and explicitly described by case studies on benchmark data. All in all, MMEASE 2.0 was unique in accomplishing comprehensive and in-depth analyses of SCM data, which could be considered as an indispensable complement to the existing tools. Now, the latest version of MMEASE is freely accessible by all users at: https://idrblab.org/mmease/.