Abstract
A series of cationic, zwitterionic and anionic fluorinated carbocyanine dyes, spin‐coated on Si substrates, were measured with time‐of‐flight static secondary ion mass spectrometry (TOF‐S‐SIMS) under Ga^+^ primary ion bombardment. Detailed fragmentation patterns were developed for all dyes measured. In the positive mode, the resulting spectra showed very intense signals for the precursor ions of the cationic dyes, whereas the protonated signals of the anionic dyes were hardly detected. Differences of three orders of magnitude were repeatedly observed for the secondary ion signal intensities of cationic and anionic dyes, respectively. All measured dyes yielded mass spectra containing several characteristic fragment ions. Although the secondary ion yields were still higher for the cationic than the anionic dye fragments, the difference was reduced to a factor of ≤10. This result and the fact that M^+^, [M + H]^+^ or [M + 2H]^+^ are even‐electron species make it very likely that the recorded fragments were not formed directly out of the (protonated) parent ions M^+^, [M + H]^+^ or [M + 2H]^+^. In the negative mode, none of the recorded spectra contained molecular information. Only signals originating from some characteristic elements of the molecules (F, Cl), the anionic counter ion signal and some low‐mass organic ions were detected. A comparative study was made between TOF‐S‐SIMS, using Ga^+^ primary ions, and other mass spectrometric techniques, namely fast atom bombardment (FAB), electrospray ionization (ESI) and matrix‐assisted laser desorption/ionization (MALDI). The measurements showed that MALDI, ESI and FAB all give rise to spectra containing molecular ion signals. ESI and FAB produced M^+^ and [M + H]^+^ signals, originating from the cationic and zwitterionic dyes, in the positive mode and M^−^ and [M − H]^−^ signals of the anionic and zwitterionic dyes in the negative mode. With MALDI, molecular ion signals were measured in both modes for all the dyes. Structural fragment ions were detected for FAB, ESI and MALDI in both the positive and negative modes. Compared with the other techniques, TOF‐S‐SIMS induced a higher degree of fragmentation. Copyright © 2005 John Wiley & Sons, Ltd.