Hydrophobic effects in the fast atom bombardment mass spectra of proteins and large peptides

The positive ion fast atom bombardment (FAB) mass spectra of a number of large peptides and small proteins are presented. The relationship between the hydrophobic character of such molecules (based on the primary amino acid sequence) and signal ion abundance observed in FAB mass spectrometry is examined, as well as the phenomenon of molecular ion suppression of large peptides by the presence of other more hydrophobic peptides in the matrix. It is concluded that the signal ion abundance of large peptides/small proteins is related to hydrophobic character and the consequences of such an observation are discussed with regard to obtaining FAB mass spectra of large peptides and proteins.