The general steps to create ion identity molecular networks

If needed, convert the spectral data files to an open format (e.g., mzML)

Import the data into one of the open source tools: MZmine, MS-DIAL, or XCMS

Process the data to create a feature list (aligned overall samples)

Perform MS¹-based feature grouping and ion identity annotation

Export the feature list as a feature quantification table (.csv), an MS² spectral summary file (.mgf), which contains a representative fragmentation spectrum for each feature, and a supplementary edges files (IIN files, .csv) (more information in the tool-specific workflow sections)

Create a metadata file to group samples for statistics (optional)

Upload all files to GNPS and start a new feature-based molecular networking job (MZmine can directly submit and start a new IIMN job on GNPS)

Download and visualize the results in a network analysis software (e.g., Cytoscape³¹, https://cytoscape.org/)

The option Download Cytoscape Data provides two.graphml networking files

The standard FBMN and IIMN networks (base directory)

IIMN networks with collapsed ion identity networks (in the gnps_molecular_network_iin_collapse_graphml directory)

The option Direct Cytoscape Preview/Download provides the IIMN network and its collapsed version as Cytoscape projects with various style presets

Refer to the documentation on how to run FBMN within GNPS and multiple mass spectrometry data processing tools.

https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking/

For IIMN, refer to the related part of the GNPS documentation.

https://ccms-ucsd.github.io/GNPSDocumentation/fbmn-iin/