Neuropeptides are diverse neuromodulators that originate in the neuroendocrine system and play important roles in many biochemical pathways. Copper toxicity is of particular interest as copper effluxes are increasing from pollution and copper is becoming more bioavailable due to ocean acidification. Characterizing neuropeptidomic changes can improve understanding of the neurochemical signaling pathways and biochemical processes involved in responding to environmental stress like copper toxicity. This dissertation explores different mass spectrometry (MS) strategies to characterize neuropeptides and related biomolecules in response to elevated copper levels with an emphasis on quantitative methods. This is performed in a crustacean model organism using custom N,N-dimethyl leucine isobaric tags (DiLeu). These tags have had extensive applications for bottom-up proteomics but have been much less explored for their application to neuropeptide quantitation due to inherent challenges in measuring these low-abundance analytes. Optimization of the MS acquisition parameters is performed to translate proteomic methods and facilitate neuropeptidomic experiments with higher throughput and broader coverage. Additionally, methods to quantify related copper-binding proteins (e.g., metallothioneins) were also developed to provide a more comprehensive understanding and multi-omic view of the underlying biochemical processes involved in copper toxicity. Overall, the work presented in this dissertation provides an improved framework for studying the functional roles of neuropeptides and proteins involved in the copper stress response.