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In MS-DIAL can process LC-MS/MS data performed in non-targeted mode, but also in MSE and now with Ion Mobility Spectrometry. After the processing the Supplementary Pairs file can be exported and used for IIN.

Development and Installation

Download the latest version of MS-DIAL software at


This work builds on the efforts of our many colleagues, please cite their work:

For IIMN: Schmid R., Petras D., Nothias LF, et al. Ion Identity Molecular Networking for mass spectrometry-based metabolomics in the GNPS Environment. Nat. Comm. 12, 3832 (2021).

For FBMN: Nothias, L.-F., Petras, D., Schmid, R. et al. Feature-based molecular networking in the GNPS analysis environment. Nat. Methods 17, 905–908 (2020).

For GNPS: Wang, M. et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat. Biotechnol. 34, 828–837 (2016).

For MS-DIAL 1): 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).

For MS-DIAL 2): 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).

Running the FBMN IIN workflow with MS-DIAL

The integration of MS-DIAL and IIN is supported since version 4.1 and support for FBMN from version 2.99. After a standard processing data with MS-DIAL, the “Alignment results” can be exported for IIN analysis.

Step 1: Process your non-targeted LC-MS/MS data with MS-DIAL following the FBMN documentation guidelines.

Step 2: After processing your data export the Supplementary Annotation/Pairs files from the "Alignement results" using the option “GNPS export” and “Export GNPS edge files”.

Step 3: Run a FBMN job and add the Supplementary Pairs file following the main IIN documentation See an example of job with IIN job with MS-DIAL

For visualizing results in Cytoscape. Please refer to the main FBMNxIIN documentation.


See our MS-DIAL tutorial on using Feature Based Molecular Networking for the American Gut Project sample.


  • Screenshots when new release available
  • Batch file for the export ?
  • Cytoscape documentation
  • Tutorial IIN


This integration was made possible by Hiroshi Tsugawa (Riken).

Page Contributions

Ming Wang (96.36%), lfnothias (3.64%)

Last update: August 11, 2021 08:51:31