Label-free differential analysis of murine postsynaptic densities

Abstract

This chapter provides detailed methodology for the enrichment and label-free differential analysis of postsynaptic density (PSD) proteins. Methods discussed will include tissue homogenization, subcellular fractionation, protein digestion, and label-free differential analysis after liquid chromatography-tandem mass spectrometry. When combined, these protocols facilitate the identi fi cation of receptors and signal transducers that comprise the PSD and provide an optimized work flow for the differential analysis of PSD proteomes. This strategy supports a utility for coupling fractionation with proteomics analysis to enrich for low-abundant proteins in cellular localizations that would otherwise be lost in a global tissue context.