Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation

Abstract

Abstract. Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B-versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant Bions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C-H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry.

Synthesis and Mass Spectrometry Analysis of Oligo-peptoids

“…For most singly charged peptoids with N-terminal acetylation, the Y-ions show much higher abundance than the B-ions 21,23 . As shown in Figure 3, except that of the B 1 -ion, the intensity of the peaks corresponding to the B-ions is much lower than those of the Y-ions.…”

“…This is a simplified structure, which helps to calculate the m/z value. The actual B-ions are likely formed in a cyclic structure, such as a five-membered oxazolone ring 23 . Not all predicted fragment ions are formed in the mass spectrometer and observed in the mass spectrum.…”

“…For peptoids with free N-terminal amino groups, higher abundance of Y-ions over B-ions has been observed as well 21 . The favoring of Y-ions suggests that the charge-carrier proton prefers to reside on the C-terminal fragments, which is due to the higher proton affinity of the C-terminal fragments 23 . In addition to the formation of B-and Y-ions, secondary fragment ions associated with water loss or labile side-chain group loss are often observed in protonated peptoids.…”

“…Our lab has adopted the method of manual peptoid synthesis and simplified the apparatus used in the existing methods. We have previously studied the fragmentation patterns of a series of peptoids using MS/MS techniques 21,22,23 . Our results show that peptoids produce characteristic fragmentations when they are subjected to collision-induced dissociation (CID) 21,23 or electron-capture dissociation (ECD) 22 experiments.…”

“…We have previously studied the fragmentation patterns of a series of peptoids using MS/MS techniques 21,22,23 . Our results show that peptoids produce characteristic fragmentations when they are subjected to collision-induced dissociation (CID) 21,23 or electron-capture dissociation (ECD) 22 experiments. In this article, we demonstrate how oligo-peptoids can be synthesized in a standard chemistry laboratory, how to perform the CID experiments using a triple-quadrupole mass spectrometer, and how to analyze the spectral data.…”