Added by Jeremy Carver, last edited by Nuno Bandeira on Sep 26, 2014  (view change)


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Need to create a new ProteoSAFe/GNPS/MassIVE account?

<Click here> for help with creating a ProteoSAFe user account.

Using FTP to transfer files to ProteoSAFe web servers

Most users prefer to use FTP to upload their files to ProteoSAFe, particularly if the files are large. Although the FTP process is slightly more involved than uploading through the ProteoSAFe web interface, it is the preferred method to ensure stable and complete uploads. It also benefits from the power of FTP to easily rename and reorganize files and folders, allowing you to create a more efficient file structure within your ProteoSAFe account's personal data space.

However, this method is only available for the official CCMS ProteoSAFe servers, for which separate FTP servers have been installed and linked to the ProteoSAFe user database. Also, this method requires the use of a registered ProteoSAFe user account - "guest" users cannot use FTP to upload their files.

To connect to your ProteoSAFe user account via FTP, simply log on to the appropriate FTP server, using the same username and password as your ProteoSAFe web account. See below for which FTP server host name to use, depending on your objective. Both official FTP servers are connected to the same user database, so your username and password will be the same for both. However, be sure to use the correct one, since they are connected to different storage servers - if you upload files to one, you will not be able to see them in the other!

ProteoSAFe/GNPS data analysis workflows MassIVE dataset submission

To do this, you will need to use your preferred FTP client program. There are many good free FTP clients, but a few of the more popular ones that have been tested with ProteoSAFe include:

CoffeeCup Free FTP

Most FTP client programs use a similar interface. There is usually some sort of "Site Manager" or "Server Manager", allowing you to set up and store your connection information for a particular FTP server, and then re-connect to that server easily. For example, in FileZilla:

Alternatively, there is usually some kind of "Quick Connect" feature allowing you to simply type in the FTP server name, your username and password, and then connect directly, such as in FileZilla:

Either method should work fine; just enter the correct address (see above) as the server or "host" name, and then your ProteoSAFe username and password, and the client should connect you to your user file space. From there, you can upload files by finding them on your computer (usually in the left panel) and then dragging them over to the server (usually in the right panel), or you can download files from the server to your computer by dragging them in the reverse direction.

You can also experiment with the FTP client interface to move and rename files and folders on the server, so as to reorganize your uploaded data in whatever manner you prefer.

If you have any questions about any part of the ProteoSAFe file upload process, please feel free to email for more information.