During the Dortmund course an instructor found it confusing in the Molecule Settings that they could check a checkbox saying "heavy" was the internal standard type, but they couldn't specify in the Quantification tab that molecules should be normalized by "Ratio to Heavy". The document did not yet have anything in the Targets view. Once they imported a transition list with heavy precursors, the "Ratio to Heavy" option was present. But, they found this confusing.

If it really doesn't make any sense to make this choice without heavy precursors in the document (though the same could be said for peptides), the option should be present and a message should be shown to the user that they need to add heavy precursors before making this selection, but that seems unnecessarily cumbersome.

I'll make it so the option is available if the document is empty.

The logic for which options show up in that list is in "NormalizationMethod.ListNormalizationMethods".
Currently that method only looks at "PeptideSettings.Modifications.HasHeavyModifications" but I'll change it so it also returns true if "SrmDocument.PrecursorCount" is zero.

This seems like a hack. In proteomics it is the IsotopLabelType that just always exists regardless of whether you have it in the document.

For small molecules it is always going to be confusing that it appears in the "Labels" tab and is checked in "Internal standard types", but is not available in the Quatification tab, even if that only happens after adding targets that don't include a heavy label.

You can't even get rid of "heavy" in the "Internal standard types" list. Maybe we should be looking at that list?