The Tool Buttons Cross-link proximity map
Cross-linking has come a long way. From simple setups with just one protein to multi subunit complexes, we can now cary out
cross-linking experiments on a large-scale basis.
In the example below, we crosslinked a homogenised murine brain (with BS3), and used the entire murine proteome for a
search space.

Obviously, the standard scan-by-scan result output is of little use against this scale, as it grows increasingly difficult to map out
just what proteins have cross-linked to what.
The cross-link proximity map lists the high-scoring proteins in your dataset.
You can then go through them one by one, and MassAI draws a neighbourhood map of the proteins cross-linked to the currently
selected protein.