The matrix effects and signal response in LC-MS analysis of six microcystins and nodularin-R were studied in mussels and liver samples from the common eider and rainbow trout. The instrumentation used in the study was a triple quadrupole MS with electrospray ionization. The results from the spiked tissue samples showed that both signal suppression and enhancement occurred. The recorded matrix effects were not severe; all studied toxins could be detected with sufficient limit of detection in all matrices. The results indicate, however, that matrix effects must be monitored for accurate quantification of microcystin and nodularin in tissue samples. Matrix effects can be studied with standard additions in the studied matrix, as was done in this study. Solid-phase extraction (SPE) resulted in a lower limit of detection compared to no cleanup in the sample preparation. SPE also prolonged the chromatographic stability. SPE cleanup is therefore strongly recommeded. Also described in this article are the chromatographic and mass spectrometric details of glutathione and cysteine conjugates, which are the detoxification products of the toxins. LC-MS analysis is suitable for detoxification studies of microcystins and nodularins. Cysteine conjugate was identified as the main detoxification product in a mussel sample that was exposed to toxic cyanobacteria in an aquarium.