Metabolomics science to elucidate the diversity of life's metabolism and its biological significance
We are the SysteMSOmics Lab, led by Dr. Hiroshi Tsugawa at the Department of Biophysical Chemistry, Kyoto University. Our name — SysteMSOmics — is a coined term combining Systems biology, MS (mass spectrometry), Omics, and Laboratory, reflecting how we bring these disciplines together to understand life.
Since our founding in 2021, we have worked to elucidate the metabolic systems of life through omics science based on mass spectrometry, spanning animals, microorganisms, and plants, by combining molecular biology, biochemistry, analytical chemistry, and informatics.
Informatics is indispensable to modern omics research. Rather than keeping our tools to ourselves, we believe progress in metabolomics and lipidomics depends on open, reproducible, and community-driven software.
- Open by default — Every tool we build is released as open source (MIT / LGPL-3.0 / CC-BY 4.0), and we publish open reference data (e.g., MassBank) so anyone can reuse, verify, and build on our work.
- Reproducibility first — We aim to give researchers not just results, but the software and tutorials needed to reproduce and extend them.
- Community-driven — We build and maintain our tools together with the global metabolomics/lipidomics community, and welcome issues, pull requests, and collaboration from anyone.
- Bridging wet and dry science — Our members work across both experimental and computational domains, so our software is designed by and for practicing scientists.
| Project | Description |
|---|---|
| MsdialWorkbench | Universal workbench incorporating MS-DIAL, MS-FINDER, and MRMPROBS — our flagship suite for untargeted/targeted metabolomics and lipidomics data analysis. |
| msdial-interactive-app | Local web workflow assistant for MS-DIAL Console, with agent and mzTab-M handoff support. |
| MSLipidMapper | Pathway-centered lipidome analysis environment linking lipid subclass, acyl-chain subsets, and multi-omics data. |
| ms2lipid | Lipid subclass prediction using machine learning and curated tandem mass spectral data. |
| msdial5tutorial | Hands-on tutorial for MS-DIAL 5, covering untargeted mass spectrometry data analysis. |
| MassBank-RDF / MassBank-data | Tools and open data contributing MassBank records as machine-readable, semantically linked resources. |
Browse all of our repositories for the full list of tools, tutorials, and data resources.
📧 Contact us: msdial-jp@googlegroups.com
This is our group mailing list and the best way to reach us for questions about any of our software, collaboration enquiries, or general discussion.
Where to go:
| If you want to... | Go to |
|---|---|
| Report a bug or request a feature | The Issues tab of the relevant repository |
| Ask how to use a tool, or anything else | msdial-jp@googlegroups.com |
| Contribute code | Open a pull request |
- Lab website: systemsomicslab.github.io
- Principal investigator: Dr. Hiroshi Tsugawa
- Department of Biophysical Chemistry, Kyoto University
We welcome collaboration, feedback, and contributions from researchers everywhere.