The role of a liquid matrix in controlling FAB-induced fragmentation.

Substantial differences were observed in terms of extent of fragmentation and type of ions in the conventional fast atom bombardment (FAB) mass spectra of peptides between different liquid matrices (such as glycerol, thioglycerol, dithiothreitol, thiodiglycol, 3-nitrobenzyl alcohol, diglyme, and sulfolane). The use of glycerol leads to extensive fragmentation. Such differences were also observed for other classes of analytes such as anthracyclines and phosphocinnamates. It is rationalized that the internal energy of the molecular ions of the analyte is controlled by desolvation of the FAB-desorbed analyte/matrix clusters. Differences in the relative abundances of the amino acid sequence determining ions were also noted. For example, in glycerol, the z-type sequence ions are more prominent for peptides containing basic amino acid residues, whereas in thioglycerol and dithiothreitol, the y-type ions dominate. These differences are correlated to the ion-dipole type of adduct formation in glycerol.