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

Abstract

The formation of c 1 ions during collision-induced fragmentation of peptides with asparagine, ornithine, or glutamine at the N-terminal position 2 has been studied. For this purpose, the corresponding fragment ion spectra of a large set of synthetic peptides were investigated. It is demonstrated that the c 1 ion intensity depends on the nature of the second residue in the N-terminal dipeptide motif as well as on the peptide length. It is shown that the formation of c 1 ions proceeds by two competing mechanisms. One mechanism is the secondary fragmentation of the b 2 ion, the efficiency of which shows only a minor dependency on the complete peptide sequence. The other mechanism is the direct formation from the molecular ion, which is identified to be connected with sequence-specific c 1 ion intensities. A model for this latter mechanism is proposed based on the analysis of the formation and secondary fragmentation of the z max-1 ion, which is the complementary ion to the c 1 ion. Additional evidence is obtained by investigation of peptides with ornithine in N-terminal position 2, which in general exhibit c 1 ion intensities intermediate between the asparagine-and glutaminecontaining species. The data presented support the reliable assignment of N-terminal dipeptide motifs using collision-induced dissociation. (J Am Soc Mass Spectrom 2010, 21, 1814 -1820

Spectroscopic Identification of Cyclic Imide b2-Ions from Peptides Containing Gln and Asn Residues

“…[46] Cyclization reactions involving the Gln sidechain N-or O-atom were suggested to occur in analogy to biological degradation of Glncontaining peptides. [47] Further evidence for such processes was found in multistage tandem MS CID experiments of b 2 -ions with Gln in the second position, where the unusual formation of a c 1 -ion was observed, [48][49][50][51] which is of interest in de novo peptide sequencing strategies. [51] Mechanistically, formation of the c 1 -ion was interpreted as evidence for the b 2 -ion having a non-oxazolone structure; in particular, it was suggested that the b 2 -ions having Gln as the second residue possess an imino-δvalerolactone structure (i.e.…”

“…[16], MS 3 data reported on Asn containing peptides is ambiguous as to the formation of c-type ions. [49,50] Energetics of imide and isoimide structures relative to the more common oxazolone and diketopiperazine motifs are significantly different for b 2 -ions produced from Asn-and Gln-containing peptides. [49] Here, we present IR spectra of b 2 -ions containing Gln and Asn residues.…”

“…[44] In other words, deviation from the formation of the classical oxazolone b 2 -ion may thus be related to the protonation site in the precursor peptide. Since Gln and Asn containing peptides have been suggested to not form oxazolone b 2 -ions [6,16,[48][49][50], we first address the question of where the proton resides in the precursor PheGlnAla peptide. Although peptides without basic residues are generally assumed to be protonated on the N-terminus, protonation of backbone amide oxygen atoms has been suggested to be competitive.…”

Investigation of c ions formed by N‐terminally charged peptides upon collision‐induced dissociation

“…However, low‐energy collision‐induced dissociation (CID) remains the most popular and readily accessible activation method for protonated peptides which is characterized by amide bond cleavage and the formation of typical b/y ions . The observation of the c‐type ion is relatively a rare event …”

Effect of the Asn side chain on the dissociation of deprotonated peptides elucidated by IRMPD spectroscopy

“…As established for protonated peptides, the side chain of Asn and Gln may become involved in the rearrangement reactions forming b 2 -type fragments [38][39][40][41][42]. It is therefore of interest to investigate what the effect of these residues is in the dissociation of deprotonated peptides.…”