Dec 09, 2025

Public workspaceUsing FileZilla to deposit data on MetaboLights V.2

This protocol is a draft, published without a DOI.
Using FileZilla to deposit data on MetaboLights
  • Sylvain Prigent1
  • 1Univ. Bordeaux, INRAE, UMR1332 BFP, 33882 Villenave d'Ornon, France
  • MetaboHUB-Bordeaux
Sylvain Prigent
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Protocol Citation: Sylvain Prigent 2025. Using FileZilla to deposit data on MetaboLights. protocols.io https://protocols.io/view/using-filezilla-to-deposit-data-on-metabolights-gzssbx6efVersion 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: May 21, 2025
Last Modified: December 09, 2025
Protocol Integer ID: 218674
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.
Troubleshooting
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
cont aining adsGo 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
WinSCP (https://winscp.net/) is another excellent file transfer tool that can also be used.



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