FBMN with MS-DIAL - Microbiome Molecules in Fecal Samples in American Gut Project
Tutorial introduction¶
In this tutorial you will be guided into running MS-DIAL for the Feature Based Molecular Network (FBMN)) workflow on GNPS to reproduce some findings of the American Gut Project described in this manuscript.
Citations¶
Recommended Citations
This work builds on the efforts and tools from our many colleagues, please cite their work:
Nothias, L.-F., Petras, D., Schmid, R. et al. Feature-based molecular networking in the GNPS analysis environment. Nat. Methods 17, 905–908 (2020).
Tsugawa, H., et al A lipidome atlas in MS-DIAL 4. Nat. Biotechnol. 38, 1159–1163 (2020).
Tsugawa, H., Cajka, T., Kind, T., Ma, Y., Higgins, B., Ikeda, K., Kanazawa, M., VanderGheynst, J., Fiehn, O. & Arita, M. MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis. Nature Methods 12, 523-526 (2015).
Lai, Z., Tsugawa, H., Wohlgemuth, G., Mehta, S., Mueller, M., Zheng, Y., Ogiwara, A., Meissen, J., Showalter, M., Takeuchi, K., Kind, T., Beal, P., Arita, M. & Fiehn, O. Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics. Nature Methods 15, 53-56 (2018).
McDonald, D. et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems 3, (2018). http://dx.doi.org/10.1128/mSystems.00031-18
Learning Objectives¶
- Learn how to download files from a GNPS/MassIVE Dataset. See instructions here.
- Run MS-DIAL feature detection on LC-MS/MS data. See tutorial here, and output a feature quantification table and a MS2 spectral file.
- Run the Feature Based Molecular Networking (FBMN) with MS-DIAL files on GNPS. See the tutorial here.
- Visualize the results of FBMN with Cytoscape See the tutorial here.
Experimental Setup¶
We will use a subset of the LC-MS/MS analysis from the American Gut Project. The samples consist of fecal samples provided by participants and the subset selected consists of participants that have high and low consumption of plants. MS-DIAL will be used to detect features and output a feature quantification table (TXT format) and a MS2 spectral file (MGF format). The feature quantification table contains the intensity values for every aligned peak accross the samples, while the MS2 spectral file contains a single MS2 representing each aligned peak.
Data and Files Needed for the Tutorial¶
LC-MS/MS data can be found in the MassIVE dataset MSV000082678. Study metadata (.TXT format) can downloaded here.
MS-DIAL representative output files¶
These files are not needed for the tutorial but are provided here as reference files, or if you wanna by pass the MS-DIAL processing.
| File Type | Download Link |
|---|---|
| Feature quantification table (TXT format) | Download |
| MS2 spectral file (MGF format) | Download |
| Study metadata (.TXT format) | Download |
| MS-DIAL project (created with version 3.64) | TODO: Download |
Required Software Installs¶
- FTP Client (e.g. WinSCP, DO NOT FileZilla!). See instructions here.
- MS-DIAL for feature detection (available only on Windows).
- An account on GNPS.
- Cytocape for network visualization.
Video Tutorial - Running MS-DIAL for FBMN¶
Running FBMN on GNPS¶
Analyzing the Results of FBMN with Cytoscape¶
Follow up Tutorial in GNPS¶
Checkout the follow up tutorial on how to do FBMN with MZmine2 and GNPS.
Other tutorials are available from the main Feature Based Molecular Networking Workflow page.