I believe that "Reference" dropdown gets populated with the values of the "Condition" replicate annotation in your document.
The idea is that this TurnoveR tool will help you compare turnover rates between different groups of replicates.
You should go to "Settings > Document Settings > Annotations" and make sure that the annotation "Condition" is checked.
Then use the "Replicates" report in the Document Grid to set the Condition for each replicate.

If your dataset does not actually have two cohorts you might be able to get away with setting the "Condition" annotation on each replicate to the same thing. I do not actually know what the TurnoveR tool will do if there is only one Condition.

By the way, the TurnoveR external tool only works with datasets that use D3 leucine. If your experiments used a different sort of heavy label, you will not be able to analyze your data using the current version of the TurnoveR tool, although they might add support for that in the future.
-- Nick