GitHub - jorainer/xcms-gnps-tools: Utility functions for the use of xcms with GNPS (original) (raw)

Utility functions for use of xcms with GNPS

Authors: Johannes Rainer, Mar Garcia-Aloy and Michael Witting.

This repository contains some utility functions to integrate xcms-based data processing into the GNPS Feature-Based Molecular Networkingworkflow (FBMN). See this pagefor details on xcms integration into FBMN, and the following GitHub repo for example scripts as Jupyter notebook and RCommander script.

The main provided functions are:

• formatSpectraForGNPS: format spectra for MGF export in the format expected by GNPS.
• getEdgelist: extract a list of edges between co-eluting ions potentially representing adducts or isotopes of the same metabolite as defined byCAMERA.
• getFeatureAnnotations: extract adduct annotations for features from aCAMERA result in the format required for Ion Identity Networking (IIN) in FBMN/GNPS.