| Abstract: | The effect of the properties of sulphur and selenium atoms, the composition and location of substituents (―CH3, ―OCH3, ―C2H5, and ―C3H6―((N+Br?)C5H5)), and the charge state on the collision induced dissociation (CID) behaviour of ions generated by electrospray ionization (ESI) of thiocarbocyanine and selenocarbocyanine dyes have been investigated. The results show that, for of all the examined singly charged ions, the main dissociation channel was related to the formation of distonic ions, generated as a result of cleavages within the dimethine bridge. In the case of doubly charged ions (with propyl‐pyridinium substituents), competition between fragmentation processes related to charges located at different nitrogen atoms has been observed. The S/Se replacement also has an impact on the CID behaviour of the examined carbocyanine dyes. On the basis of the performed CID MS/MS experiments, general rules for the CID of thiocarbocyanine and selenocarbocyanine dyes have been proposed. |
