Described herein are methods, systems, and compositions for detecting enzyme activity. In some embodiments, the reaction product(s) are coupled with a mass tag, and the enzyme activity is determiner by analyzing the reaction product(s). The enzyme assays can be performed using mass spectrometry, for example nanostructure-initiator mass spectrometry (NIMS). Also described are methods, systems, and compositions for monitoring enzymatic degradation process of a substrate sample, for example a biomass.