Proteins and other biomolecules such as lipids are significant players in the central nervous system and are implicated in various neurological disorders. Their identification, quantification, and distribution are thus important not only in understanding the disease but also in developing treatments. A combined workflow allowing the localized microextraction of discrete regions identified by a matrix-assisted laser desorption/ionization mass spectrometry (MSI) imaging experiment for proteomics analysis by liquid chromatography/tandem mass spectrometry (LC MS/MS) is described in this chapter. MSI was initially used to map lipid distributions allowing for the identification of regions of interest (ROIs) that are then subjected to microextraction in a consecutive tissue section. Mounting of consecutive tissue on parafilm allows microdissection of the ROIs, where proteins can then be recovered for processing and LC MS/MS analysis. The PAM method provides a fast and cheap means to perform further downstream analysis after an MSI experiment.