This study offers a unique insight into the mass accuracy and resolving power requirements in MS/MS analyses of complex product ion spectra. In the examples presented here, accurate mass assignments were often difficult because of multiple isobaric interferences and centroid mass shifts. The question then arose whether the resolving power of a medium-resolution quadrupole time-of flight (QqTOF) is sufficient or high-resolution Fourier-transform ion cyclotron resonance (FT-ICR) is required for unambiguous assignments of elemental compositions. For the comparison, two paralytic shellfish poisons (PSP), saxitoxin (STX) and neosaxitoxin (NEO), with molecular weights of 299 and 315 g·mol Ϫ1 , respectively, were chosen because of the high peak density in their MS/MS spectra. The assessment of QqTOF collision-induced dissociation spectra and FT-ICR infrared multiphoton dissociation spectra revealed that several intrinsic dissociation pathways leading to isobaric fragment ions could not be resolved with the QqTOF instrument and required FT-ICR to distinguish very close mass differences. The second major source of interferences was M ϩ 1 species originating from coactivated 13 C 12 C cϪ1 ion contributions of the protonated molecules of the PSPs. The problem in QqTOF MS results from internal mass calibration when the MH ϩ ions of analyte and mass calibrant are activated at the same time in the collision or trapping cell. Although FT-ICR MS readily resolved these interfering species, the QqTOF did not provide resolving power Ͼ20,000 (full width at half maximum) required to separate most isobaric species. We were able to develop a semi-internal QqTOF calibration technique that activated only the isolated 12 C isotope species of the protonated molecules, thus reducing the M ϩ 1 interferences significantly. In terms of overall automated elemental formulas assignment, FT-ICR MS achieved the first formula hit for 100% of the product ions, whereas the QqTOF MS hit rate was only 56 and 65% for STX and NEO product ions, respectively. External mass calibration from commercial FT-ICR and QqTOF instruments gave similar results. ass-based structural identification of drugs and their metabolites frequently employs combinations of collision-induced dissociation (CID) analyses on triple quadrupole and ion trap mass analyzers. These methods often provide adequate information for determining the sites of modification for structural analogs [1][2][3][4][5]. In those cases, however, in which the variety of fragment ions is limited and the spectra do not allow unambiguous structure assignments, tentatively identified structures are often further examined by high-resolution mass spectrometry, from which elemental compositions can be obtained. In these experiments, it is required to measure the mass-tocharge ratios with the smallest mass uncertainties possible, in particular if the methodologies are part of routine structure identification protocols. Ideally, unattended and automated analytical routines with sufficient resolution and mass accu...