8/31/2023 0 Comments Peptide backbone nitrogen atom![]() More recently, Morishetti and co-workers studied the influence of the nature of the charge (alkali vs proton) on the peptoid ion dissociation in the gas phase. Interestingly, when comparing isomeric peptide/peptoid, the relative abundance of the y/Y fragment ions is most of the time higher from protonated peptoids than from peptide ions. Note that the b/y sequence ions are capitalized for the peptoid sequence ions. When submitted to collisional activation, both kinds of ions dissociate at the amide bond leading to the formation of b/y and B/Y sequence fragment ions. compared the fragmentation patterns of peptide ions and their peptoid analogs. The mass differences between two successive sequence ions, i.e., ions which arise from the backbone cleavage, provide information on the amino acid sequence. In the context of peptides, MS methods are widely used to determine the amino acid sequence, paving the way to the high throughput collision-induced dissociation (CID) sequencing of peptides and proteins. Mass spectrometry (MS) represents an elegant way to elucidate the primary structure of compounds provided that they can be transferred/ionized in the gas phase of the mass spectrometer. They determined that the length of the hydrophobic sequence impacts the mechanical properties and the structure of the nanotubes, including their diameter and their thickness. studied the formation of stiff nanotubes from sequence-defined peptoids. They demonstrated that the helical conformation of peptoids is dictated by the specific position and number of the chiral monomer units. ![]() Shin and co-workers investigated the influence of the achiral/chiral monomer sequence on the conformation of peptoid heptamers in solution using circular dichroism. Synthetic strategies to finely tune the peptoid sequence are now abundantly exploited to master the secondary structure of peptoids to target applications, such as chiral sensors, biomimetics, or piezoelectric devices. Due to the large diversity of commercially available amines, the number of accessible structures is in principle infinite and can vary in terms of the nature of the side chains and their sequence. Efficient synthetic protocols are now available and are basically based on a stepwise incorporation of the peptoid residues. The main difference between peptoids and peptides lies in the side chain position in the building block, located respectively on the nitrogen atom rather than on the α-carbon. Poly- N-substituted glycines, better known as peptoids, represent a class of synthetic polymers which are closely related to peptides (Scheme 1). The consecutive and competitive characters of the A 1-Y x and the B/Y mechanisms are also investigated by drift time-aligned CID experiments. Whereas the production of Y x ions from acetylated peptoids also involves the B/Y pathway, the observation of abundant Y x ions from non-acetylated peptoid ions is shown in the present study to arise from an A 1-Y x mechanism. Dissociation of the ion/neutral complex predominantly produces Y ions due to the high proton affinity of the secondary amide function characteristic of truncated peptoids. Upon the nucleophilic attack of the oxygen atom of the N-terminal adjacent carbonyl group on the carbonyl carbon atom of the protonated amide, the peptoid ions directly dissociate to form an ion-neutral complex associating an oxazolone ion to the neutral truncated peptoid residue. We demonstrated that the B/Y cleavages of collisionally activated O-protonated peptoids must involve the amide nitrogen protonated structures as the dissociating species, mimicking the CID behavior of protonated peptides. Here we revisit this backbone cleavage mechanism by performing CID and ion mobility experiments, together with computational chemistry, on tailor-made peptoids. Previous papers proposed that protonated peptoids dissociate following an oxazolone-ring mechanism starting from the O-protonation species and leading to high mass Y sequence ions. However, the knowledge of the ion fragmentation patterns say the dissociation reaction mechanisms is a prerequisite to reconstitute the sequence based on fragment ions. Mass spectrometric techniques and more particularly collision-induced dissociation (CID) experiments represent a powerful method for the determination of the primary sequence of (bio)molecules. ![]()
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