Neuropeptidomics: The characterization of neuropeptides and hormones in the nervous and neuroendocrine systems

While genome characterization has become routine, characterizing the final biologically active protein products resulting from gene expression still takes considerable effort, especially for neuropeptides. Neuropeptides and hormones, the bioactive products of prohormone gene, are an important and ancient class of cell-to-cell signaling molecules. They primarily work as neuromodulators but can also act as neurotransmitters and hormones, affecting functional sites far removed from their point of synthesis or release. One of the goals of neuropeptidomics is the wholesale characterization of neuropeptides, but there are several issues to consider when choosing a measurement strategy. First, because many neuropeptides act at low concentrations, their characterization requires a technique with low detection limits. Moreover, their physiological effects depend on the exact chemical form of the peptide, and peptides are often altered by posttranslational modifications. Therefore, an information-rich detection scheme that can provide details on molecular structure with high specificity is required. Lastly, details on localization and temporal changes are often needed to infer the functional significance of newly discovered peptides. Although no one approach fits all of these requirements, mass spectrometry (MS) is widely employed to characterize neuropeptides as it allows structural characterization and quantitation without requiring analyte preselection, features that provide opportunities to study known and unexpected peptides at both the organismal and cellular levels. We describe the MS-based techniques used to interrogate and discover neuropeptides, how they are implemented in synergy with other methods for probing the biological functions of identified neuropeptides, and provide a range of examples of neuropeptide discovery within the mammalian circadian system.