Isotope labeling and quantitative LC-MS profiling together offer a promising approach for unraveling dynamics of biosynthesis of specialized metabolites (natural products) in plants and other organisms. Isotope patterns and ratios in metabolites harbor valuable information tracing the biosynthetic history of specific compounds. This technique provides a promising tool for extending metabolic flux analyses to complex specialized metabolites in a wide range of organisms. However, the isotopic patterns of highly labeled metabolites can exhibit remarkable complexity, and therefore accurate and high-throughput data processing is necessitated when analyzing labeling of large numbers of metabolites in biological matrices. Here we demonstrate how a new approach based on spectral deconvolution achieves simultaneous quantification of complex isotope patterns of 13C-labeled natural products.