Post-translational modifications (PTMs) play important roles in modulating biological functions of proteins. Stoichiometry, which quantifies the modification percentage, is a critical factor for any given PTM. In this work, we developed a chemoproteomic strategy called “STO-MS” to systematically quantify the PTM stoichiometry in complex biological samples. This strategy employs a resolvable mass tag to differentiate proteoforms with different number of modifications, and utilizes liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) techniques to measure PTM stoichiometry at the proteomic level.