<jats:title>Abstract</jats:title><jats:p>The development of reliable analytic methods, capable of separating mixtures of secondary metabolites as well as providing structural information, is essential for the investigation of secondary metabolites, e.g. from <jats:italic>Streptomyces</jats:italic>. Here we report a liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI‐MS/MS) method using a triple quadrupole mass analyzer for the structural elucidation of caprazamycins and liposidomycins from culture extracts of the wild‐type producer strains. Comparison of the fragmentation patterns in positive as well as in negative ionization mode revealed several characteristic product ions used for identification of six new caprazamycins. Furthermore, a chromatographic method for the purification of nucleosides from cell cultures using a boronic acid gel was adapted for the partial purification of the culture extracts. Copyright © 2011 John Wiley & Sons, Ltd.