The analysis and quantitation of neurologically-relevant molecules requires detection methods that are sensitive, selective, and applicable to a wide range of molecules. Targeted analysis using tandem mass spectrometry allows for the detection of molecules from complex matrices with an added level of selectivity. Mass spectrometry is on the leading edge of technological advances and improvements in our understanding of the intricate workings of the brain, allowing us to develop better models and better therapeutic approaches. In this thesis, I use tandem mass spectrometry to investigate two classes of neurochemicals: classical neurotransmitters, and potential therapeutic drugs based on endogenous neuropeptides. Chapter 1 will introduce exis...