Hi Will,

As you've seen, the assay.AssayList is a query that provides a filtered view of the exp.protocol table from the underlying database.

You should be able to use XML metadata to configure the lookup from your column to the AssayList table. I was able to get this to work for me locally, with XML like this:

<tables xmlns="http://labkey.org/data/xml">
  <table tableName="AssayLookup" tableDbType="NOT_IN_DB">
    <columns>
      <column columnName="Lookup">
        <fk>
          <fkDbSchema>assay</fkDbSchema>
          <fkTable>AssayList</fkTable>
          <fkColumnName>RowId</fkColumnName>
        </fk>
      </column>
    </columns>
  </table>
</tables>

How are you trying to apply your metadata? Via the schema-level XML in a module? As a .query.xml file in a module? Through the schema browser? I think that the schema-level approach will likely not work (as it would be trying to target an assay.assaylist table in the actual database) but the others should work.
Thanks,
Josh