Yeast Fermentation with YPD + Apple Juice
Thank you for an especially clear and detailed question!


  For YPD + apple juice fermentation, I was thinking of doing the same procedure with 50 mL YPD + 50 mL apple juice in each "special flask". Will this work? 


I think this would work but it seems like a better comparison to your earlier experiments to keep using 50 mL of total medium, i.e., mix 25 mL of YPD with 25 mL of apple juice.  That way the volume of the fermentation is the same in each experiment.


  Will this be good for the same HPLC setting?


Probably, although it depends on the components of the apple juice you use.  Have you injected just apple juice (unfermented) into your HPLC?  Have you verified that this negative control injection contains no ethanol or other interfering peaks in the region of interest?  If not, those are things you should do to make sure the HPLC method you have developed for YPD medium will still work in apple juice-based media.