A number of unique challenges are inherent to the study of neuropeptides (NPs), both in determining their molecular structure and their function. Traditional studies follow a model in which novel NPs are discovered and identified, then investigated for function. These studies frequently use biochemical techniques that can be imprecise and cumbersome. Mass spectrometry (MS)-based tools are becoming important not only in precisely determining the identity of a NP or quantifying a compound with a known sequence, but also in studies where identity and putative function can be determined simultaneously. Tools based on MS and tandem MS (MS/MS) have been developed, both with isotope labeling strategies and label-free methods, that allow accurate quantitation of NP changes associated with behavior or physiological manipulation, concurrent with identification of sequence. MS and MS/MS have also been implemented with sampling methods that incorporate temporal or spatial information while determining functional role of a NP, such as microdialysis (MD) and imaging mass spectrometry (IMS). These advances in MS and sampling techniques allow investigation of a particular biological phenomenon to guide studies aimed to identify and characterize NPs. Permitting function to drive identification of relevant compounds allows for a broader understanding of the molecular underpinnings of these events. The NPs thus identified can then be validated with more conventional techniques, and successive iterations of identification and function determination will provide rich information about these compounds. This function-driven discovery of NPs using MS-based techniques is an important new approach for their study.