Hi! Have you think on doing HPLC analysis? This method can help you to quantify glucose and fructose separatedly in a precise way.

Article Development and validation of a liquid chromatographic metho...

to my knowledge, when you are using absorbance based methods, then it cannot be possible to discriminate among the two reducing sugars

Dear Matan,

Generally, I agree with Diana for HPLC method. As an alternative method you could try enzyme/colorimetric method. It specific and relativelly fast for realysation. Because of specifity, the method is suggested for analysis of mixture of them in foodstuffs, beverages and other materials (https://secure.megazyme.com/Sucrose-Fructose-D-Glucose-Assay-Kit)!

Hope to be helpful and I wish you success in your task!

Sincerely,

Manol

You can use a kinetic method with chemiluminescence detection. Check the article below:

Article Determination of glucose and fructose in mixtures by a kinet...