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 (b(n)) arise after the C-terminus is lost as an intact amino acid or peptide; further loss of CO leads to immonium ions (a(n)). Upon generation of C-terminal sequence ions (y(n)), 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 greater-than-or-equal-to 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.