Characterization of unknown synthetic by-products from a test synthesis of the experimental inhibitor of HIV-1 reverse transcriptase, BI-RG-587, is presented. Seven impurities were separated and characterized by thermospray liquid chromatography/mass spectrometry using low-resolution, high-resolution, and B/E linked scanning methods. The high-resolution mass measurements which were obtained were accurate to within 10 ppm of structures proposed for synthetic by-products present at the 0.1% level. Linked scans produced daughter ion spectra for each impurity to further aid in the characterization.