Skip to content


Molecular Networking

Q: My molecule of interest is not appearing in my classical molecular networking. What should I do?


  1. Ensure Inclusion: First, make sure that your molecule is included in the network and not filtered out by the minimum cluster size setting (the default is 2).
  2. Check for Neighbors: Next, check if your molecule has any neighboring connections in the network.
  3. Examine Singletons: To be thorough, examine the network including singletons.

Q: I have a ton of data to analyze at GNPS2 but the File Uploader is slow, how do I get my data over there?


GNPS2 has an FTP/SFTP upload portal that is meant for close collaborators to be able to upload a significant amount of data. Otherwise, since GNPS2 does not have the ability to store massive amounts of data for the broader community, we recommend deposition of the data at a public repository such as MassIVE in order to do analysis of such data at GNPS2.