Ion Identity Networking (IIN)


The Ion Identity Networking (IIN) workflow complements the Feature-Based Molecular Networking (FBMN) by grouping MS2 spectra not only through similarity of MS2 spectra, but also of MS2 spectra whose precursor ions fulfill the retention time, peak shape, user-defined. It enables the visualization of patterns of ion species and brings together subnetwork from the same molecule to create an ion identity molecular family. IIN can be performed with MZmine, XCMS-CAMERA, or MS-DIAL.

Finally, we apologize for the crudeness at parts of IIN documentation as it is currently a work in progress.


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

For IIN: Schmid et al. In preparation.

For FBMN: Nothias, L.F. et al Feature-based Molecular Networking in the GNPS Analysis Environment bioRxiv 812404 (2019).

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).

And the tools you used to process your data.

Running the IIN workflow

The Ion Identity Networking workflow is run throught the FBMN workflow by providing Supplementary Annotation/Pairs files in the "Advanced Extras" panel of the standard FBMN workflow interface.


Alternatively, the quickstart interface for FBMN can also be used:


Note that multiple Supplementary Pairs files can specified. Their content will be added.

Generating Supplementary Pairs

The Supplementary Annotations/Pairs files can be generated with the following software:

Alternatively, the results of other software could be used as long as the LC-MS feature identifier (ID) matches the "SCANS=" number in the MGF file.

Supplementary pairs

The Supplementary Pairs is a .CSV format file (coma separated), and must contains the following columns:

Header Description
ID1 Node ID 1 matching the row IDs
ID2 Node ID 2 matching the row IDs
EdgeType Any string describing the type of edge
Score A numerical value for the score (cannot be empty)
Annotation A string annotation

See an example of the Supplementary Pairs used in the Ion Identity Networking (IIN) workflow


Exploring the IIN workflow in Cytoscape



  • Cytoscape documentation

Page contributors

Robin Schmid (WWU, Münster, Germany), Daniel Petras (UCSD), Louis Felix Nothias (UCSD), Ming Wang (UCSD).