Export/Submit to GNPS-FBMN

Description

The GNPS Export/Submit module exports all files needed for Feature-Based Molecular Networking on the GNPS web-platform. This includes the feature quantification table (CSV file) and the MS/MS spectral summary (.MGF file) with representative MS/MS spectra for the row in Aligned Peaklist. Optionally, a new GNPS job is submitted. This job can either be directly linked with a GNPS user profile (username and password are optional) or can be cloned into a personal GNPS account later on.

IMPORTANT for the "Submit to GNPS" option:

Instructions

Run this method on any Aligned Peak List. MS/MS spectra need to be associated to the features (usually done in the peak deconvolution step).

Parameters

Filename
Base name for the output files
Mass list
Select the masslist that contains MS2 scans (and MS1 for the Merge MS/MS option)
Merge MS/MS (Experimental)
The Merge MS/MS option enables to merge MS2 spectra associated to an LC-MS feature (or LC-MS peak) in one representative MS/MS spectrum. In this mode, the precursor ion purity is evaluated using MS1 scans, and the MS2 spectra are merged using various options. See our preprint for more informations.
Filter rows
Limit the exported rows to be included in the MS/MS spectral summary file (.MGF). Default is "ONLY WITH MS2 or ANNOTATION"
Submit to GNPS
Directly submit a job to GNPS for rapid analysis. This job can either be directly linked with a GNPS user profile (username and password are optional) or can be cloned into a personal GNPS account later on. IMPORTANT: files are not served on the GNPS. See above disclaimer.

Open folder
Opens the folder containing the output files

Documentation

Please refer to the following documentation for a detailed tutorial: