We present the design and synthesis of a new quantitative strategy termed Soluble Polymer-based Isotope Labeling (SoPIL) and its application as a novel and inclusive method for the identification and relative quantification of individual proteins in complex snake venoms. The SoPIL reagent selectively captures and isolates cysteine-containing peptides, and the subsequent tagged peptides are released and analyzed using nanoflow liquid chromatography-tandem mass spectrometry. The SoPIL strategy was used to quantify venom proteins from two pairs of venomous snakes; Crotalus scutulatus scutulatus type A, C. s. scutulatus type B, C. o. helleri, and B. colombiensis. The hemorrhagic, hemolytic, clotting ability and fibrinogenolytic activities of crude venoms were measured and correlated with difference in protein abundance determined by the SoPIL analysis. The SoPIL approach could provide an efficient and widely applicable tool for quantitative proteomics.