Tandem mass spectrometry of peptides with N-terminal glutamine studies on a prion protein peptide

This paper reports the unusual collision-induced fragmentation of peptides having N-terminal glutamine. One of these glutamine-containing peptides was isolated from an endo-proteinase Lys-C digest of the scrapie prion protein (PrP 27–30) with the predicted sequence QHTVTTTTK. Daughter ion mass spectra show predominant N-terminal a n b n and, to a lesser extent, c n sequence ion series at 17 u less than the predicted masses. This is interpreted as arising from an ionic fragmentation that accompanies the peptide-backbone cleavage, glutamine losing ammonia to give pyroglutamic acid, a reaction that parallels the commonly observed solution-phase process. This behavior is less evident when strongly basic residues near the C-terminus cause the C-terminal fragments (x n, y n, and z n ) to predominate.