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
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.
The Supplementary Pairs is a .CSV format file (coma separated), and must contains the following columns:
|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
TO DO NOTES
- Cytoscape documentation
Robin Schmid (WWU, Münster, Germany), Daniel Petras (UCSD), Louis Felix Nothias (UCSD), Ming Wang (UCSD).