The dissociation reactions of indocyanine green (also known as cardiogreen) have been studied in a Fourier-transform ion-cyclotron resonance mass spectrometer by the application of unimolecular, collision-induced dissociation and photodissociation using femtosecond laser pulses. Ions were prepared by electrospray ionization (ESI) in various solvents. Depending on the properties of the solvent mixture, the mono sodiated molecule could be measured through cation exchange in various compositions. Using a mixture of methanol/water/formic acid as solvent, protonated ions, formed by exchange of sodium, are predominantly observed. A mixture of isopropanol/formic acid leads to the addition of a further sodium cation to the molecule yielding an intense bi-sodiated ion signal. The photodissociation of the stored ions was achieved using pulses at a wavelength of 790 nm and approximately 150 fs pulse duration. The results show that only fs-photodissociation leads to the fragmentation of the different molecular structures, while in case of sodiated indocyanine green collision induced dissociation fails completely to observe any fragments. In all other investigated ion structures, the collision-induced-dissociation spectra show unspecified and little intense spectra. It is shown that fs-photodissociation mass spectrometry is the only method that leads to substance specific fragmentation for this sample. Furthermore, indocyanine green is known to form aggregation products. In the ion-cyclotron resonance experiment, the reactions of a dimeric cluster were also investigated. The necessary condition and the interference of the fragmentations with those of the monomer are discussed.

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