Fragmentation Pathways Of Peptides And Their Isomers In Tandem Mass Spectrometry

Tandem mass spectrometry plays an important role in the studies of peptide identification as well as proteomics.Some peptides consist of the same amino acid but have different structures due to the presence of amino acid isomers,such as the participation of Asp.The Asp residue can shift from L to D or ? to ? conformation in biological condition.The conformational changes always increase structural diversity and influence biological activity.For example,the biological activities of neuropeptides are related to the presence of chiral amino acids.Protonated peptides are often used for peptide identification in tandem mass spectrometry,while sodiated peptides give different conformation and different fragmentation patterns,which benefit to the peptide identification of some specific amino acid.In this thesis,we studied the fragmentation of sodiated peptides upon collision induced dissociation(CID)in tandem mass spectrometry experiments and used quantum chemical calculations to rationalize fragmentation pathways of particular amino acids.We also studied the fragmentation of chiral peptides that affected by adding proton,sodium ion and cucurbituril molecular and showed the efficiency for the identification of chiral amino acid in peptides.The thesis contains two parts shown in the followings:1.Comparison of the fragmentation of glutathione(GSH)and its isomer ECG in tandem mass spectrometry.Cysteine and serine residue have similar side chain but give different fragmentation patterns in sodiated peptides.Glutathione(GSH)is a natural peptide with a unique amide bond formed between the side chain of glutamic acid and the amine group of cysteine residue,its isomer ECG is a normal peptide.We performed CID on both sodiated and protonated GSH and ECG under the same condition,and found a characteristic neutral loss of 45 Da corresponding to NH3 plus CO for sodiated GSH,as well as an abnormal ion b1(b1-H+Na).The proposed mechanism is a two-step process and a cyclic ester is the intermediate.Theoretical calculations were used to rationalize the reaction intermediate and the generation of [M+Na-NH3-CO] + ion.2.Fragmentation of D-amino acid-containing peptides using tandem mass spectrometry.D-amino acid-containing peptides(DAACPs)have been proved to be bioactive in living systems.In this study,we focus on neuropeptides,which always have a D-amino acid at the second position in the sequence.We studied their fragmentation patterns when associated with a proton?sodium ion and cucurbituril molecular.We found that the relative intensity of b ion is affected by the conformation of the amino acid when they associated with proton and cucurbituril.The use of noncovalent complexes proved an effective method to determine epimers in tandem mass spectrometry.In summary,on the basis of the characteristic fragmentation ion of the sodiated GSH,we can confirm the structure of GSH.The host–guest interaction of the peptides and cucurbituril gives out unique fragment ions in the gas phase thus the D isomeric amino acids can be identified qualitatively.We hope these specific fragmentation pathways and methods can be applied to improve the accuracy of protein identification.