Streptomycin (SM) is composed of streptidine, streptose and N-methyl glucosamine sugar moieties. For the determination of SM and its related substances, an ion-pair LC-UV detection method using a Supelcosil LC-ABZ column was developed previously. While analyzing commercial samples, several unknown compounds were detected. Most of these compounds are not yet characterized. In this study, the above LC method was coupled to MS for impurity profiling in a selected commercial sample. However, it could not be directly coupled to MS due to the presence of the nonvolatile salt, buffer and ion-pair reagent in the mobile phase. So, for structural characterization, each peak eluted from the nonvolatile eluent system was collected and transferred to MS after the desalting process. In total, 16 compounds were studied, 15 compounds including 12 unknowns could be identified.