An approach to the differentiation of leucine and isoleucine residues in EI mass spectra of peptides

Residues of leucine and isoleucine cannot generally be distinguished in the electron impact (EI) generated mass spectra of N-acylated peptide esters. We have obtained the mass spectra of model peptide esters containing leucine or isoleucine in various positions and trifluoroacetyl perdeutero leucine as the N-terminal blocking group. The mass spectra of the peptide derivatives show a pair of peaks as a result of the elimination from the M⁺ ion of neutral fragment of perdeuterated isobutene (M⁺-64) from the leucine side chain of the N-terminal blocking group and isobutene or butene (M⁺-56) from leucine or isoleucine residues of the peptide. The ratios of the intensities of the peaks $\text{M}{}^{\mathrm{+}}\text{-56}\text{M}{}^{\mathrm{+}}\text{-64}$ show considerable variation with the position of leucine or isoleucine in the peptide chain and the length of the peptide, but for peptides which are identical except for the fact that one contains leucine and the other isoleucine in a given position the ratio is always smaller for the isoleucine containing peptide. The differences are sufficient to distinguish the isomeric residues if comparison spectra are available.