Date of Award


Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Pharmaceutical and Chemical Sciences

First Advisor

Jianhua Ren

First Committee Member

Skylar Carlson

Second Committee Member

Xin Guo

Third Committee Member

Qinliang Zhao


Peptoids are versatile compounds exhibiting many applications in various fields ranging from polymeric science to drug development. Combinatorial libraries are a powerful tool for exploring various applications of peptoids. Among robust analytical tools, tandem mass spectrometry is a method of choice to decode the sequence of unknown peptoids in combinatorial libraries. In this study, we have synthesized peptoids with various side chains and found interesting fragmentation pathways. The introduction to my research and methods used for the experiments are discussed in detail in chapters one and two, respectively.In chapter three of this dissertation, a systematic study of acetylated peptoids with positioning of a basic sidechain at various locations has been conducted using a linear ion trap mass spectrometer. The fragmentation characteristics of peptoids charged with metal ions, such as Li+ and Na+, are compared with those of the protonated peptoids. The acetylated peptoids without any basic sidechain were taken as a reference. It has been found that metal ions assist in increasing the formation of N-terminal fragment ions due to chelating between the metal ions and the peptide fragments. In addition, metal ions enhances ionization efficiency of peptoids without charge trapping sites. In the fourth chapter, new fragmentation pathways of peptoids are proposed and tested. To investigate the mechanism of water loss from peptoid fragment ion, a linear ion trap mass spectrometer was used to perform tandem fragmentation experiments on selected peptoids. The absence of certain fragment ions toward the N-terminus suggests that water loss occurs through a five-membered ring intermediate instead of a six-membered ring. The fragmentation of peptoid backbone mainly yields the B- and Y-ions through an oxazolone ring intermediate. The Y-ions are formed by abstraction of a proton from the oxazolone ring, which is essentially the proton from the alpha position of the dissociating amide bond. In nonacetylated peptoids, an oxazolone ring is absent during the formation of terminal Y-ions. The mechanism behind the appearance of terminal Y-ions have been studied using deuterium labeled peptoids. Fragmentation experiments on deuterium labeled peptoids indicates that the proton is not abstracted from the alpha position. The likely proton source is the hydrogen on the amine group of the N-terminus. The comparison of fragmentation patterns between peptoids containing acidic and basic sidechains is documented in the last chapter of this dissertation. Carboxyl group on the sidechain does not appear to influence the favorable formation of C-terminal ions. Considerable abundance of low-mass B-ions is explained by a cascade secondary fragmentation of high-mass B-ions. The fragment ions formed using the linear ion trap instrument show a considerable abundance of high mass Y-ions. While fragmentation experiments using tandem quadrupole instrument show high intensity of low mass ions which are possibly formed from secondary fragmentation of high mass ions. This study will aid in understanding the nature of fragmentation behavior of peptoids and support the discovery of unknown sequences. As peptoids closely resemble peptides, the findings from this work will help to complement the fragmentation mechanism of peptides.



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