Yeah I was thinking temperature. For example, you're not supposed to use boiling water for green tea, as it burns the tea. I've noticed this with many brands, however each brand tends to be a bit different - some are more tolerant to higher temperatures than others.

I imagine you can also do a multi-stage extraction, where you heat at a lower temperature and then at a higher temperature. This should avoid denaturing the lower temp compounds. It's commonly done with alcohol when extracting sugars into the wort.