Measuring the percent crystallinity of the biomass samples is particularly important as it affects rate and yield of enzymatic saccharification (Hall et al. 2010). It is challenging to measure the percent crystallinity of the biomass using DSC, as cellulose decomposes even before it undergoes melting (Paul et al. 2010; Kaloustian et al. 2003; Soares et al. 1995). As enthalpy of crystallization and enthalpy of melting are required to find the percent crystallinity of the sample, it is not possible to measure percent crystallinity of the biomass based on this technique. However, the enthalpy of dehydration of cellulose and biomass samples has been correlated to percent cellulose crystallinity of the samples based on the hydrogen bonds formed by the crystalline and amorphous cellulose. A detailed method for measuring cellulose crystallinity (CC) by DSC has been reported by Bertran and Dale (1986). They have reported that DSC provides a better way of measuring CC than other traditional approaches like XRD, especially for substance with very low crystallinity index. The amount of moisture absorbed by cellulose containing substances is dependent on the amount of crystalline and amorphous cellulose present in the substance. Amorphous cellulose absorbs a high amount of moisture while pure crystalline cellulose has no absorption capacity. Hence the endothermic dehydration peak appearing in DSC thermograms can be used to estimate the percent crystallinity of the cellulose present in the substances. Using completely amorphous cellulose measured under the same experimental conditions, the percent CC of the sample can be estimated from the following equation where AH0 is the heat of dehydration for a completely amorphous cellulose sample and AHs is the heat required to dehydrate the sample.

In spite of the many advantages of using TGA and DSC analysis they cannot be used to find bond specific information about the substrate. Knowledge of the chemical composition of the substrate is required ahead of time. Analysis through this technique always requires one to correlate the original substrate to the pure components of the substrate. The changes to DP of a polymer can only be visualized but cannot be quantitatively correlated to changes in the molecular weight of the polymer. Also if the substrates decompose very close to each other, we cannot differentiate between the increase of one of the substrate or decrease in DP of the polymer degrading at a higher temperature. As these techniques affect the samples physically and chemically the sample used in this technique cannot be recovered or reused.