Neuropeptides represent the most complex group of endogenous molecules in the nervous system that plays important roles in the regulation of physiological process. Elucidation of these signaling molecules is a crucial step towards understanding the underlying mechanism of neuromodulation. My thesis research focuses on development of an efficient peptide discovery pipeline that accelerates neuropeptidomic analysis in crustacean models.;We established a high-definition MS approach for identification and characterization of large crustacean hyperglycemic hormone (CHH)-family neuropeptides, which was achieved by combining bottom-up, off-line top-down, and on-line top-down tandem MS methods. We further refined and incorporated this high-definition approach into a multi-scale strategy for simultaneous and confident sequence elucidation of various sizes of peptides in the crustacean nervous system. A wide range of neuropeptides with various molecular weights (0.9-8.2 kDa) were fully sequenced.;The well-characterized primary sequences of neuropeptides provide opportunities for elucidation of their structural information. To rapidly and precisely localize D-amino acids in bioactive peptides, we developed a novel site-specific strategy by ion mobility spectrometry (IMS) analysis of MS-generated epimeric fragment ions. Our results indicate that the isomerization of L- to D-Phe occurs in the American lobster CHHs. In addition to characterization of conformational isomers of neuropeptides, our method allows elucidating structural isomers in gas phase. We report on a novel strategy for qualitative and quantitative analysis of b-type ion isomers by combining electron transfer dissociation, IMS and formaldehyde labeling. The analysis results provide evidence to support the proposed fragmentation mechanism of peptide sequence scrambling in gas phase.;The final goal of our study is to understand the roles of neuropeptides play in neural circuits. To investigate if CHHs are involved in regulation of food intake, a new isotopic labeling-assisted top-down MS strategy was developed to directly monitor the abundance changes of endogenous large neuropeptides. Comparative analysis in unfed and fed crabs revealed that the CHH abundance in the sinus glands was significantly increased after food intake. In addition, label-free quantitative analysis reveals that the orcokinin and RFamide peptides were down-regulated after food intake, suggesting that the release of these neuropeptides might be altered by feeding behavior.
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