Mass spectrometry, in particular MALDI-MS, has often been used as a valuable means to characterize dendritic molecules with respect to their molecular masses. Also, it is a valuable tool for analyzing potential defects in their structure which result from incomplete synthetic steps. This article presents a comparison of ESI and MALDI mass spectrometric experiments on dendrimers persulfonylated at their periphery. While the ESI mass spectra easily permit impurities and defects to be identified and thus provide evidence for sample purity, reactions with acidic matrices occur during the MALDI process. The resulting defects are identical to those expected from incomplete substitution. Thus, in these cases, MALDI-MS yields false negative results. With mass-selected, ESI-generated ions, collision experiments were performed in an FT-ICR mass spectrometer cell to provide detailed insight into the fragmentation patterns of the various dendrimers. Different fragmentation patterns are observed depending on the exact structure of the dendrimer. Also, the nature of the charge is important. The fragmentation reactions for protonated species differ much from those binding a sodium or potassium ion. These differences can be traced back to different sites for binding H+ versus Na+ or K+. Tandem MS experiments on mass-selected dendrimer ions with defects can be used to distinguish different types of defects. A concise structural assignment can thus be made on the basis of these experiments. Even mixtures of two isobaric defect variants with the same elemental composition can be identified.