Clusters consisting of a few atoms build the bridge between individual atoms and the condensed phase of matter and they are, thus, of great general interest. Over the last two decades, considerable progress has been made in the study of their properties and ion storage techniques, in particular the use of ion cyclotron resonance (Penning) traps, are important tools for advanced investigations. Vice versa, cluster ions can serve as probes for the evaluation of ion-trap properties. Furthermore, they are ideally suited for the calibration of mass spectrometers and for consistency checks in high-accuracy mass determinations. Examples from the research areas mentioned, i.e. the investigation of cluster properties and the application of cluster ions for Penning-trap studies and mass calibration, are reported.