Quantitative proteomics is a powerful and versatile tool for studies of biological systems. In this work, quantitative proteomics was applied to the discovery of candidate cargoes for a novel endocytic pathway (FEME) and in the characterisation of a murine model of motor neurodegeneration. In-gel digestion and On-bead digestion strategies were compared for their capacity to generate quantitative data from a plasma membrane fraction. This data was used to identify Junction Plakoglobin, Dysferlin and others as candidate FEME associated proteins for future study. The suitability of In-gel digestion and filter-aided sample preparation coupled to strong cation exchange (FASP-SCX) was evaluated in the context of capturing a whole tissue proteome from mouse spinal cord. This data showed a downregulation of proteins involved in neuron differentiation, neurogenesis and neuron development in juvenile mice lacking functional HSJl protein, helping to characterise the events which precede neuron death and highlighting candidate HSJl client proteins.