The neutral products formed during backbone fragmentations of protonated peptides in tandem mass spectrometry.

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 neutralization-reionization mass spectrometry (NRMS). N-terminal acylium ions (bn) arise after the C-terminus is lost as an intact amino acid or peptide; further loss of CO leads to immonium ions (an). Upon generation of C-terminal sequence ions (yn), a hydrogen atom attached to a nitrogen rearranges from the N-terminal to the C-terminal side yielding a protonated amino acid (y1) or peptide (y > or = 2) as the ionic fragment; the complementary neutral fragment is an aziridinone if the N-terminal amino acid is cleaved and a diketopiperazine if two N-terminal amino acid units are eliminated. Detection of neutral dissociation products can reveal valuable structure information, as demonstrated with the tetrapeptides Val-Gly-Ser-Glu and Val-Gly-Asp-Glu.