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<!DOCTYPE html>
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<title>MZmine 3 - Ion Identity Networking and Feature-based Molecular Networking</title>
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<h2><strong>Ion Identity Molecular Networking</strong> and <strong>Feature-based Molecular Networking</strong> on the GNPS web-platform</h2>
MZmine offers an export for all files needed for molecular networking, e.g., performed by the IIMN workflow
(<a href="https://www.nature.com/articles/s41467-021-23953-9" target="_blank">reference paper</a>) or the FBMN workflow
(<a href="https://www.nature.com/articles/s41592-020-0933-6" target="_blank">reference paper</a>) on
<a href="https://gnps.ucsd.edu/" target="_blank">GNPS</a>. The export is also used by other tools as described in the
<a href="https://mzmine.github.io/mzmine_documentation/tool_integration.html" target="_blank">documentation</a>.
Extensive documentation for IIMN and FBMN is available on the
<a href="https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking/" target="_blank">GNPS documentation site.</a>.
<br/><br/>
Ion Identity Networking (IIN) in MZmine adds a new way to connect features in molecular networks,
based on MS1 analysis of ion species (different adducts and in-source fragments of the same compound).
Refer to <a href="https://ccms-ucsd.github.io/GNPSDocumentation/fbmn-iin" target="_blank">this part of the GNPS documentation</a>
on how to combine IIN and FBMN within MZmine and GNPS. IIMN is now in the MZmine 3 release. Get instructions on getting the latest
version under <a href="download.html">download</a>.<br/>
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