Cyanobacterial toxins as microcystins (MCs), nodularins (NODs), Paralytic Shellfish Poisoning (PSP) toxins, anatoxins (ANAs), and cylindrospermopsins (CYNs) with over 100 known varieties, occur worldwide associated with human and animal lethal poisoning.In contrast to all analytical methods for toxin determination are based on LC/MS-MS measurements with Multiple Reaction Monitoring (MRM) the application of Precursor Ion mode allows the coverage of all these structural variants. Although in MRM mode enables a higher sensitivity, a lot of information regarding structural changes is missed. The new generation of Q-TRAPs combines the advantages of quadrupoles having a high selectivity with the high sensitivity of ion-trap systems. Here we published results, showing the suitability of Precursor Ion mode for detection of cyanobacterial toxins extracted from phytoplankton.