To describe a high-performance separation of spectinomycin and its biosynthetically related compounds using ion-pairing reversed-phase liquid chromatography (IP-RPLC). The separation is performed on a Thermo Scientific™ Acclaim™ AmG C18 column, packed with a novel C18 bonded silica phase specially designed for separation of aminoglycoside antibiotics under acidic conditions. In these separations pentafluoropropionic acid (PFPA) and heptafluorobutyric acid (HFBA) are used in the mobile phase to enhance the retention and optimize the separation of all detected components.