The Feature-Based Molecular Networking (FBMN) workflow 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 the mzTab-M format.
The main documentation for Feature-Based Molecular Networking with XCMS can be accessed here. See our preprint Nothias, L.F. et al bioRxiv 812404 (2019).
This repository contains example scripts in Python and R showing how XCMS version >= 3 (XCMS3) can be used for the
FBMN workflow in GNPS using a subset of samples of the American Gut Project (MSV000082678) and soil bacteria (MSV000079204).
Install the latest version of XCMS3 (version >= 3.4) from Bioconductor in R with:
install("BiocManager")
BiocManager::install("xcms")
For more information, also refer to the xcms Bioconductor package.
For utility functions specific to this workflow refer to the Github repository: https://github.com/jorainer/xcms-gnps-tools.
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).
https://github.com/sneumann/xcms
Tautenhahn R, Boettcher C, Neumann S. Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformatics, 9:504 (2008).
Smith, C.A., Want, E.J., O'Maille, G., Abagyan,R., Siuzdak, G. XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification.. Analytical Chemistry, 78, 779–787 (2006).
The main documentation for Feature-Based Molecular Networking with GNPS can be accessed here.
The XCMS-GNPS integration was developed by Johannes Rainer and Michael Witting, in coordination with Louis-Félix Nothias and Daniel Petras. This tutorial was prepared by Madeleine Ernst and Ricardo da Silva.