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FBMN with MetaboScape

Introduction

The Feature-Based Molecular Networking (FBMN) is a computational method that bridges popular mass spectrometry data processing tools for LC-MS/MS and molecular networking analysis on GNPS. The tools supported are: MZmine2, OpenMS, MS-DIAL, MetaboScape, XCMS, and Progenesis QI.

The main documentation for FBMN can be accessed here.

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

Using MetaboScape and the Feature-Based Molecular Networking

MetaboScape can be used to process LC-MS/MS Bruker Daltonics data files (.d file). 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] (http://dorresteinappshub.ucsd.edu:5050/featurebasednetworking) or the standard interface of the FBMN workflow (you need to be logged in GNPS first).

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

A. Perform Feature Detection with Profile Analysis

  1. Open Profile Analysis and perform feature detection on your data following Profile Analysis documentation to generate the 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.
  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.

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  1. Right-click on the Bucket Table and select Export to GNPS format (.mgf/.csv).

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  1. Select Export all formats.

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  1. The .mgf file ('gnps.mgf') and the Bucket Table will be used to perform a Feature-Based Molecular Networking job on GNPS (see below).

C. Perform FBMN Job on GNPS

Go to GNPS to perform a FBMN job. Refer to that documentation.

D. 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 contributors

Louis Felix Nothias (UCSD), Tam Dang (Tech. Univ. Berlin), Kevin Ngoc (UCSD).

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