Journal of the American Society for Mass Spectrometry

, Volume 15, Issue 12, pp 1810-1819

First online:

Fragmentation of protonated oligoalanines: Amide bond cleavage and beyond

  • Alex G. HarrisonAffiliated withDepartment of Chemistry, University of Toronto Email author 
  • , Alex B. YoungAffiliated withDepartment of Chemistry, University of Toronto


The fragmentation reactions of the singly-protonated oligoalanines trialanine to hexaalanine have been studied using energy-resolved mass spectrometry in MS2 and MS3 experiments. The primary fragmentation reactions are rationalized in terms of the bx-yz pathway of amide bond cleavage which results in formation of a proton-bound complex of an oxazolone and a peptide/amino acid; on decomposition of this complex the species of higher proton affinity preferentially retains the proton. For protonated pentaalanine and protonated hexaalanine the major primary fragmentation reaction involves cleavage of the C-terminal amide bond to form the appropriate b ion. The lower mass b ions originate largely, if not completely, by further fragmentation of the initially formed b ion. MS3 energy-resolved experiments clearly show the fragmentation sequence bn → bn−1 → bn−2. A more minor pathway for the alanines involves the sequence bn → an → bn−1 → bn−2. The a5 ion formed from hexaalanine loses, in part, NH3 to begin the sequence of fragmentation reactions a5 → a*5 → a*4 → a*3 where a*n = an−NH3. The a*3 ion also is formed from the b3 ion by the sequence b3 → a3 → a*3 with the final step being sufficiently facile that the a3 ion is not observed with significant intensity in CID mass spectra. A cyclic structure is proposed for the a*3 ion.