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Collisionally activated dissociation (CAD) of the protonated polyalanines Ala-Ala, Ala-Ala-Ala, and Ala-Ala-Ala-Ala causes breakup of the peptide bonds leading to sequence-indicative fragment ions. The neutral molecules eliminated during these reactions are identified here using neutral-ization-reionization mass spectrometry (NRMS). N-terminal acylium ions (b „) arise after the C-terminus is lost as an intact amino acid or peptide; further loss of CO leads to immonium ions (a „). Upon generation of C-terminal sequence ions (y „), a hydrogen atom attached to a nitrogen rearranges from the N-terminal to the C-terminal side yielding a protonated amino acid (yi) or peptide (y> 2) as the ionic fragment; the complementary neutral frag-ment is an aziridinone if the N-terminalamino acid is cleaved and a diketopiperazine if two N-terminal amino acid units are eliminated. De-tection of neutral dissociation products can reveal …