Positive and negative ion fast atom bombardment ( f.a.b .) mass spectrometry were found to be useful methods for the analysis and structural characterization of five Nα-(t- butoxycarbonyl )-O-( diorganylphosphono )-L- serines ( organyl = Ph, Et, Me, Bzl , But), especially in the case of the sensitive benzyl and t-butyl phosphono derivatives. Under positive ion operating conditions, high intensity pseudo-molecular ions were obtained in the f.a.b . mass spectra, and the fragmentation pathway of the phenyl, ethyl and methyl derivatives was established by parent/daughter linked scanning studies to involve (a) the two-step loss of the t- butoxycarbonyl group, (b) loss of the amino acid as the neutral fragment from the [MH]+, [MH-56]+, [MH-100]+ and [MH-146]+ ions by a four- centred β-elimination rearrangement, and (c) cleavage of the phosphono phenyl and ethyl groups from only the [(RO)2P(OH)2]+ and [NH=CHCH2PO3R2+H]+ fragments. Parent/daughter linked scanning studies of the benzyl derivative showed that the prominent fragmentation involved loss of the benzyl group as the tropylium ion and that the 'apparent' [MH-90]+ peak observed in its f.a.b. mass spectrum resulted from cleavage of the phosphono benzyl group in the matrix during the bombardment process. In the case of the t-butyl derivative, parent/daughter linked scanning studies showed that the prominent fragmentation involved successive 'in-flight' loss of the phosphono t-butyl groups as isobutene. Negative ion f.a.b. mass spectrometry of the five derivatives gave f.a.b. mass spectra which displayed distinct [M-H]- anions along with high intensity [M-H-R]- and [(RO)2PO2]- fragment anions, the f.a.b . mass spectrum of the t-butyl derivative containing an additional [M-H-But-But]- fragment anion. Parent/daughter linked scanning studies established that the majority of the observed fragment anions resulted from extensive fragmentation of the Boc -Ser(PO3R2)-OH derivatives in the matrix phase followed by sputtering of the resultant fragments into the gas phase. In addition, positive ion f.a.b . mass spectrometry was found to be useful for the analysis of a series of protected O-( diorganylphosphono ) seryl-containing dipeptides and tripeptides ( organyl = Ph, Et, Me, Bzl ). The obtained spectra showed that β-elimination fragmentation of the Ser(PO3R2) residue was more pronounced with the tripeptide series and indicated that there was increased sensitivity of the O-( diorganylphosphono ) seryl residue with replacement of the Boc group by an amino acyl residue at its N-terminus.
