Tandem mass spectrometry of peptides. III—differentiation between leucine and isoleucine based on neutral losses

The neutral species generated during the collisionally activated dissociation (CAD) of the protonated dipeptides Ala–Leu, Ala–Ile, Leu–Ala and Ile–Ala are post‐ionized by collision and detected in neutral fragment‐reionization (+NfR+) mass spectra. These spectra are dominated by fragment ions diagnostic for the C‐terminal amino acid, as confirmed by comparison with reference collision‐induced dissociative ionization (CIDI) mass spectra of authentic Ala, Leu and Ile. CIDI of Leu and Ile yields distinct and structurally indicative products. These are also observed upon +NfR+ of [Ala–Leu]H+ and [Ala–Ile]H+, respectively, thus allowing one to deduce the correct sequence. In contrast, [Leu–Ala]H+ and [Ile–Ala]H+, which possess identical C‐termini, form no differentiating neutral losses upon CAD.