Jun 09, 2026
Version 3
Using FileZilla to deposit data on MetaboLights V.3
This protocol is a draft, published without a DOI.
- 1Univ. Bordeaux, INRAE, UMR1332 BFP, 33882 Villenave d'Ornon, France
- MetaboHUB-Bordeaux
Protocol Citation: Sylvain Prigent 2026. Using FileZilla to deposit data on MetaboLights. protocols.io https://dx.doi.org/Version created by Sylvain Prigent
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: June 09, 2026
Last Modified: June 09, 2026
Protocol Integer ID: 318770
Keywords: FTP, File transfer, MetaboLights, data deposition workflow for metabolight, metabolomics data to the metabolights repository, metabolights repository, metabolomics data, datasets into metabolight, data on metabolight, metabolights documentation, using filezilla, metabolight, straightforward ftp, based data deposition workflow, transferring file, processed dataset
Funders Acknowledgements:
MetaboHUB
Grant ID: ANR-11-INBS-0010
PHENOME
Grant ID: ANR-11-INBS-0012
MetEx
Grant ID: ANR-21-ESRE-0035
Abstract
A straightforward FTP-based data deposition workflow for MetaboLights using FileZilla.
This protocol describes the step-by-step procedure (site setup, authentication, directory navigation, transferring files) to upload metabolomics data to the MetaboLights repository.
By following this protocol, users can deposit their raw and processed datasets into MetaboLights.
MetaboLights documentation: https://www.ebi.ac.uk/metabolights/editor/guides/Files/Upload
Image Attribution
All the images in this protocol have been created by the authors specifically for this protocol.
Materials
A computer or server with a Windows, MacOS or Linux distribution, with internet access. An admin account might be needed to install FileZilla if it's not already installed.
Before start
Check that you have a MetaboLights account and that you are listed as an author with modification access in the repository you want to upload data to.
Install FileZilla - if not done previously
Go to https://filezilla-project.org/download.php?show_all=1 and choose the installer for your system.
Note
Caution is advised with the FileZilla website if you don't use the link above. The green ‘click here’ buttons lead to a file containing ads that might be flagged by antivirus software.
Note
Install the software
Connect yourself on MetaboLights
When you want to upload data on MetaboLights (for example to upload an Assay file, bellow) click on the upload button
You will get the following menu opening
Choose "Private FTP Upload"
A new window will open with your connection information
Those information will be used to connect to the MetaboLights server, to upload your files there
Open the FileZilla software and locate where the connection information must be entered (purple box).
FileZilla contains two main panes: the red box shows the files on your local computer, while the cyan box shows the files on the remote computer (in our case, the MetaboLights server once you are connected).
Enter the information in FileZilla using the following mapping
Then click on "Quickconnect", you are now connected to the MetaboLights servers and a list of directories should have appeared on the right side of the window
Transfer data to MetaboLights
Go to the folder of your study in MetaboLights by copy/pasting the "Remote folder" information into the field bellow. Press "Enter" on your keyboard.
From there, use the left panel (green bellow) of the software to navigate to the folder on your computer containing the files you want to transfer.
To transfer files just drag and drop them in the right part of the software (blue)
Success! The file has been transferred
Synchronize the modifications in Metabolights
Depending if you uploaded Metadata or Data files, click on the corresponding button in the "Files" tab to synchronise your data and have them on you Metabolights interface
Acknowledgements
Thanks to M. Peteira for the usefull comments