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FBMN with MetaboScape


The main documentation for Feature-Based Molecular Networking (FBMN) can be accessed here. See our preprint on bioaRxiv.

Below we describe how to use MetaboScape with the FBMN workflow on GNPS.

Citations and development

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

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

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).

Using MetaboScape and FBMN

MetaboScape can be used to process LC-MS/MS Bruker Daltonics data files (i.e. *.d files). After the processing with MetaboScape, the output files can be used to run the Feature-Based Molecular Networking workflow on GNPS either using the [Superquick FBMN start page] ( or the standard interface of the FBMN workflow (you need to be logged in to GNPS first).

Requirements: Install MetaboScape (at least version 2.0) and get a valid license.

A. Perform Feature Detection with Profile Analysis

Nontargeted LC-MS/MS

  1. Open Profile Analysis and perform feature detection on your data following Profile Analysis documentation to generate an ion feature bucket table.
  2. Define groups and/or attributes to enhance downstream data analysis (see 3.3.4 in the MetaboScape 2.0 tutorial documentation). The groups and/or attributes defined in Profile Analysis will be visualized in the molecular networks using pie chart diagram.
  3. IMPORTANT: Create one common group named 'SAMPLE' for all the samples. It will be used for molecular networking visualization.
  4. Export the bucket table to MetaboScape (see 3.1 in the MetaboScape 2.0 tutorial documentation).

B. Use MetaboScape to Annotate MS/MS spectra

  1. Open MetaboScape.
  2. Open the project in MetaboScape (see 3.7 in MetaboScape 2.0 tutorial documentation).
  3. Assign MS/MS spectra to the bucket table (see 3.7 in MetaboScape 2.0 tutorial documentation).
  4. Sort buckets based on the presence of MS/MS.
  5. Select only the buckets that have MS/MS associated with them.
  6. Perform Automatic molecular formula generation using SmartFormula (see 3.11.1 in MetaboScape 2.0 tutorial documentation) on these buckets. Make sure to select Selected buckets only.
  7. Search molecular formula with SmartFormula.


  1. Right-click on the bucket table and select Export to GNPS format (.MGF/.CSV).


  1. Select Export all formats.


  1. The MS/MS spectral summary (.MGF file) and the feature quantification table (.CSV file) will be used to perform a FBMN job on GNPS (see below).

Processing IMS Data (PASEF)

The FBMN supports Ion Mobility Spectrometry (IMS) Data acquired in data-dependent acquisition mode using Parallel Accumulation-Serial Fragmentation (PASEF) and processed with MetaboScape (ver. 5.0). Process the IMS data following the MetaboScape documentation and do Export to GNPS format as indicated above. The cross collission section values and other annotations can be subsequently mapped in Cytoscape.

See a representative FBMN job made from PASEF data (timsTOF) processed with MetaboScape (ver. 5.0). The Bruker files are available on the following MassIVE deposition (MSV000084402)

C. Perform FBMN Job on GNPS

Go to GNPS and perform a FBMN job. Refer to that documentation. For metadata format supported, see this page


D. Map MetaboScape Annotation in Cytoscape

See the step-by-step tutorial using MetaboScape 2.0 and the FBMN for more details.

Step-by-Step Tutorial

See the step-by-step tutorial using MetaboScape 2.0 and the FBMN for the Coffee tutorial (part of the MetaboScape 2.0 documentation).


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Page Contributions

Ming Wang (7.41%), lfnothias (50.62%), Ivan Protsyuk (7.41%), tamhdang (34.57%)

Last update: June 13, 2020 23:18:29