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Cell-to-cell signaling molecules are an important class of endogenous molecules which are responsible for cell-to-cell communication within organisms. Small molecules and peptides work as neurotransmitters and neuromodulators in the nervous system and play important regulatory roles in a wide range of physiological events and animal behaviors, such as pain sensation, food intake, memory, circadian rhythm, tissue regeneration and drug addiction. Cell-to-cell signaling molecules are highly diverse in structure or sequence and their quantities are different at various time points or locations in the nervous system. In addition, cell-to-cell signaling molecules are usually expressed in relatively low abundance level in cells. All these features make the characterization of cell-to-cell signaling molecules a challenging task. Multiple methods have been successfully applied to study cell-to-cell signaling molecules in different animal models. Mass spectrometry (MS), with the assistance of improved sampling and separation techniques, can reveal identity and structure of cell-to-cell signaling molecules and also provide insight into their changes in different biological processes. Various sample types are used in the study of cell-to-cell signaling molecules, such as cell releasates, tissues and biological fluids. This often requires an optimized use of an MS platform or a combination of them, depending on the practical situation and research goal. In this dissertation, four different MS platforms which cover both electrospray ionization (ESI) and matrix assisted laser desorption/ionization (MALDI) were used to characterize cell-to-cell signaling molecules secreted by or contained in animal models of rotifers, mice and rats in both a targeted and untargeted manner. For targeted studies, a separation protocol or detection channel is established and optimized specifically for one or a few molecules of interest, whose functions or involvements in certain biological processes are known. For untargeted studies, MS is usually coupled with bioinformatics for peptide identification or integrated with statistics for comparative quantitation. Findings from these studies help facilitate our understanding of cell-to-cell communications in different animal models. In addition, the work presented in this dissertation also includes development of novel analytical methods and evaluation of different sampling methods, which represent a contribution in the aspect of methodology. Sweedler, Jonathan V. Sweedler, Jonathan V. Newmark, Phillip A. Mitchell, Douglas A. Yau, Peter M. Yang, Ning 2017-03-01T17:00:50Z 2017-03-01T17:00:50Z 2019-03-02T10:15:21Z 2016-09-02 2016-12 Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2018-12-01 The student, Ning Yang, accepted the attached license on 2016-08-28 at 16:06. The student, Ning Yang, submitted this Dissertation for approval on 2016-08-28 at 16:18. This Dissertation was approved for publication on 2016-09-02 at 08:46. DSpace SAF Submission Ingestion Package generated from Vireo submission #10131 on 2017-02-28 at 14:40:45 Made available in DSpace on 2017-03-01T17:00:50Z (GMT). No. of bitstreams: 2 YANG-DISSERTATION-2016.pdf: 4614948 bytes, checksum: c8f6497609c5532e4b61092d9fa7be55 (MD5) LICENSE.txt: 4206 bytes, checksum: e90c3d626c374e9b15dd190d47d36d36 (MD5) Previous issue date: 2016-09-02 Embargo set by: Seth Robbins for item 98657 Lift date: 2019-03-01T17:02:22Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system Embargo set by: Seth Robbins for item 98657 Lift date: 2019-03-01T17:03:32Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system Embargo set by: Seth Robbins for item 98657 Lift date: 2019-03-01T17:05:02Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system Embargo set by: Seth Robbins for item 98657 Lift date: 2019-03-01T17:06:55Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system Limited Restriction Lifted for Item 98657 on 2019-03-02T10:15:21Z. application/pdf http://hdl.handle.net/2142/95541 en Copyright 2016 Ning Yang mass spectrometry neuropeptide signaling molecules peptidomics structure elucidation Mass spectrometry-based characterization of cell-to-cell signaling molecules in the nervous system text text Chemistry Chemistry University of Illinois at Urbana-Champaign Dissertation Ph.D.