The fragmentation reactions of protonated oligoalanines (trialanine, tetraalanine and pentaalanine) and the fragments present in the electrospray ionization (ESI) mass spectrum of polyalanine have been studied by collisionally activated dissociation (CAD) mass spectrometry (MS2 and MS3 experiments). The MSn experiments provided strong evidence that the m/z 71n + 1 ion series in the ESI mass spectrum of polyalanine is a bn series. These ions are formed via the bn–ym pathway of amide bond cleavage, which results in the formation of a proton-bound complex of an oxazolone and a peptide/amino acid. Also, the MS2 spectra of the bn series from polyalanine revealed that the chain length of bn ions influences significantly the dissociations taking place. For example, bn ions start losing H2O at n ≥5 and the losses of CO and CO + NH3 decrease in intensity from b2 to b15. The elimination of H2O + NH3 and the elimination of 61 mass (HN = C = O + H2O) commence with b6; their abundances initially increase up to ~ b8–b9 and then gradually decrease until b15 (largest fragment studied). The tandem mass spectrometry experiments help to elucidate the dissociation mechanisms of the observed structures of biopolymer fragments. Copyright © 2011 John Wiley & Sons, Ltd.