Formation of c₁ fragment ions in collision‐induced dissociation of glutamine‐containing peptide ions: a tip for de novo sequencing

Abstract

A c1 ion was observed with significant yield in the tandem mass (MS/MS) spectra of peptide ions containing glutamine as the second amino acid residue from the N-terminus. The c1 fragment was generated independently of the N-terminal residue of the peptide, but its abundance was strongly dependent on the side-chain identity. This ion is not a common fragmentation product in low-energy collision-induced dissociation of peptide ions, but it assists in identification of the first two amino acid residues, often difficult due to a low or absent signal from the heaviest y ion. A consecutive fragmentation mechanism is proposed, involving a b2 ion with a six-membered ring as an intermediate, to explain the exceptional stability of the c1 fragment ion. The utility of this information is discussed, especially in de novo sequencing of peptide ions.

Structural and mechanistic information on c1 ion formation in collision-induced fragmentation of peptides

“…Contrary to this observation, the fragmentation behavior of b 2 ions carrying Q is consistently positiondependent, which confirms the model introduced by Lee, Y. J. and Lee, Y. M. [8]. A feature left unanswered by these studies is the variable intensity of the c 1 ion in different types of synthetic peptides.…”

“…The differences indicate that the b 2 ion with the sequence QY and YQ exhibit different structures in the gas-phase. The structure of the b 2 ion QY is probably an oxazolone or diketopiperazine structure [10], while the b 2 ion YQ presumably is of the structure proposed [8]. Apart from this, the fragmentation behavior of the synthetic peptides with N in position 1 and 2 is nearly identical (see Figure 1 c/d).…”

“…As this mechanism does not involve the carbonyl group as suggested [8], the fragmentation of peptides with ornithine (O) in N-terminal position 2 should lead to the formation of a c 1 ion as well. To investigate this further, three peptides were synthesized composed of the N-terminal dipeptide motif LO and the three core sequences.…”

“…The formation of c 1 ions for peptides with Q in N-terminal position 2 was described using a set of 11 synthetic peptides representing 10 different sequences for the N-terminal dipeptide motif [8]. In this study, the authors propose a mechanism for the formation of c 1 ions by secondary fragmentation of the b 2 ion.…”

“…Due to this lack of fragmentation between the first two residues, comprehensive interpretation of low mass fragment ions in peptide CID spectra is required for unique sequence information about the N-terminal dipeptide motif, which otherwise is a blind region in peptide sequencing by CID [6,7]. Another less extensively studied terminal fragmentation process is the formation of c 1 ions, which so far has only been reported for selected N-terminal dipeptide motifs with glutamine in position 2 [8].…”