Structure and reactivity of a_n and a*_n peptide fragments investigated using isotope labeling, tandem mass spectrometry, and density functional theory calculations

Abstract

Extensive 15 N labeling and multiple-stage tandem mass spectrometry were used to investigate the fragmentation pathways of the model peptide FGGFL during low-energy collisioninduced-dissociation (CID) in an ion-trap mass spectrometer. Of particular interest was formation of a 4 from b 4 and a 4 * (a 4 -NH 3 ) from a 4 ions correspondingly, and apparent rearrangement and scrambling of peptide sequence during CID. It is suggested that the original FGGF oxa b 4 structure undergoes b-type scrambling to form GGFF oxa . These two isomers fragment further by elimination of CO and 14 NH 3 or 15 NH 3 to form the corresponding a 4 and a 4 * isomers, respectively. For ( 15 N-F)GGFL and FGG( 15 N-F)L the a 4 * ion population appears as two distinct peaks separated by 1 mass unit. These two peaks could be separated and fragmented individually in subsequent CID stages to provide a useful tool for exploration of potential mechanisms along the a 4 ¡ a 4 * pathway reported previously in the literature . In most MS/MS experiments, protonated peptides are excited collisionally to induce dissociation (collision-induced-dissociation, CID) and the fragment ion spectrum is used to elucidate peptide sequences. The CID spectra of peptides in proteomics studies are commonly assigned by bioinformatics tools that implement sequencing algorithms and peptide fragmentation models. Regrettably, the existing sequencing programs are based on rather limited fragmentation models that poorly approximate the rich dissociation chemistry of protonated peptides [3]. These limitations often lead to erroneous assignment of peptides and proteins, and the resulting uncertainty in the evaluation of the raw MS/MS data is one of the major limiting factors in large-scale protein identification studies [4,5]. The incorporation of more detailed peptide fragmentation mechanisms and spectral characteristics into these sequencing algorithms would undoubtedly place MS/MS based sequencing on a much more robust basis.In general, fragmentation of protonated peptides under low-energy collision conditions involves protondriven reactions in which amide bonds are cleaved along the peptide backbone and b, y, and a ions [6,7] are formed. The energetics and kinetics of the necessary proton mobilization (mobile proton model [8,9]) and amide bond cleavage pathways [3, 10 -14] have received significant research interest. On the other hand, much less attention has been devoted to the structure and reactivity of the primary fragments formed by backbone cleavages. According to the recent pathways in competition (PIC) fragmentation model [3], the thermodynamic properties and the reactivity of these fragAddress reprint requests to Dr. M. Van Stipdonk,

Rearrangement Pathways of the a4 Ion of Protonated YGGFL Characterized by IR Spectroscopy and Modeling

“…While this chemistry becomes facile for b 5 and larger ions, IR spectroscopy [9] of the b 4 ion of protonated YGGFL suggests that at least a small fraction of the b 4 ion population is present as the macrocyclic isomer. Labeling studies support this finding for a 4 and a 5 ions [32]. Ring-opening of this structure can lead in principle to three additional linear oxazolones GGFY oxa , GFYG oxa , and FYGG oxa ; the first of these is energetically more favorable than the YGGF oxa [9,32].…”

“…a n Ions are formed [5,6,[29][30][31][32] mainly [33] from b n ions by elimination of CO. According to theory, this reaction proceeds from the linear, oxazoloneterminated b n ion isomer, initially leading to the linear, protonated imine (-HN + =CHR n ) terminated a n ion isomer.…”

Cyclization of peptide b9 ions

“…Again in agreement with the earlier study, the acetylated peptide shows essentially no a or a* ions in fragmentation of the b 9 or MH ϩ ions. A number of recent studies [16,30,33,37,40,41] have established that a ions have more than one structure including a cyclic structure. Formation of such a cyclic structure requires a free N-terminal amino group with the result that such cyclization is not possible for the acetylated peptide.…”

“…Such a cyclization apparently plays a major role in the formation of stable a ions. Formation of a* ions by loss of NH 3 from a ions also requires a free N-terminal amino group [37,40,41] and is blocked by the N-terminal acetylation.…”

“…(Stable b 4 ions appear to undergo only minor cyclization [15,16], although CID studies [37] suggest a much greater extent of cyclization for activated ions before fragmentation.) Although there is some evidence for at least partial cyclization of larger b ions [27,28,34], no systematic study has been carried out to probe the extent of full cyclization of larger b ions.…”