Frequently asked questions

General

What is SNAP-MS?

SNAP-MS is a tool for predicting the compound families for groups of mass spectrometry features. It is most commonly used to annotate molecular networking graphs, but can also be used to annotate MS features grouped by other methods (e.g. UV spectrum similarity).

How do I get started?

To get started go to the SNAP-MS webserver and either enter a list of masses in the text box, or drag and drop a molecular networking file.

How much does it cost to use SNAP-MS?

Nothing! SNAP-MS is open source and free to use. If you would like the source code you can find it at github.com/liningtonlab/snapms. The Dockerized local version is also available at this site.

Do I need to register to use SNAP-MS?

No. The system is free and open. You only need to register for the NP Atlas site if you would like to submit new compounds or additions/ corrections (which we encourage you to do!).

Applications

Can you view the original feature ID in the separate graphml files?

We keep the componentindex value as the linkage between the original MN subnetwork and the results networks so that you can see which compound families go with which MN subnetworks. However, SNAP-MS only predicts compound family for each MN subnetwork, not the specific identities of each node. In other words, it can tell you what class of compounds is in each subnetwork, but not which member of the family each node belongs to. This is because we are only using MS1 distributions to find compound families, so can’t differentiate between (for example) two nodes with the same MS1. To do that you would have to use other tools to more closely interrogate the MS2 data for specific nodes.

Technical details

My molecular networking file is too large for the webserver. What can I do?

For very large graphs we recommend installing the tool locally. SNAP-MS is encapsulated in a Docker container, making deployment relatively easy. Basic instructions for local deployment are available in the README.MD file.