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:
- The password is sent without encryption (until the server has moved to its final location with https).
- The input files uploaded to GNPS with the "Submit to GNPS" option are not saved on your GNPS user account. These files are deleted on monthly basis, which prevent futur cloning of the job and retrieval of the files. Use the "standard" interface of the FBMN for persistant jobs and more options.
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:
- If you use the GNPS Export/Submit please cite:
- See the documentation about FBMN with MZmine on GNPS, and how to perform molecular networking, MS/MS spectral library search, and benefit from other tools available in GNPS environment.
- Or check out the youtube playlist on important steps for FBMN within MZmine and direct submission of the data to GNPS.