Tandem mass spectrometry studies of protonated and alkali metalated peptoids: Enhanced sequence coverage by metal cation addition

Abstract

The fragmentation characteristics of five oligo-peptoids were studied under tandem mass spectrometry conditions. The charged peptoids were produced by protonation and alkali metal cation (Li +, Na +, K +, Rb +, and Cs +) addition. The peptoids were ionized by the MALDI process and the resulting ions were fragmented via collision-induced dissociation (CID) experiments. All charged peptoids fragmented predominantly at the amide bonds. Highly abundant and sequence-dependent fragment ions were observed. The fragmentation patterns for the protonated peptoids and the metal cation adducts were strikingly different. All protonated peptoids fragmented by producing predominantly Y-type ions. The bias towards Y-ions was largely due to the greater proton affinity of the secondary amine at the terminal side of the Y-ions. All alkali metalated peptoids fragmented by producing both Y′- and B′-type ions, suggesting a “mobile metal cation” mechanism. For the peptoids with basic side chains, formation of the most abundant ions corresponded to the cleavage of the amide bonds at or near the basic residue. These results suggest that the metal cations are largely coordinated to the side chain of the basic residue. Chelation between the metal cation and the amino groups of the peptoids is an important factor to stabilize the fragment ions. For the peptoid without a basic side chain, the ion intensity was evenly distributed among all medium sized fragment ions. Fragmentations of protonated and alkali metalated peptoids yielded complementary sequential information, which demonstrated the practical utility of using mass spectrometry methods for de novo sequencing of peptoid libraries generated by combinatorial chemistry.