Efficient production of biodiesel from microalgae requires analysis of all cell products, including carbohydrates, lipids, and proteins. A complete characterization of the carbohydrate breakdown products is essential for nutrient recycling to determine which sugars are best absorbed by the algae. Carbohydrate content in microalgal biomass often contains complex mixtures of C5 and C6 sugars, requiring a separation technique with high resolution and high sensitivity.