Unbiased proteomic study of the axons of cultured rat cortical neurons

We have conducted quantitative proteomic analyses of the axons of cultured rat cortical neurons. Axons are isolated by using glass chips that enable the axons and their cell bodies of neurons to grow in separated regions on the chip surface. Proteins extracted from the isolated axons, as well as those extracted from whole cortical neurons are subjected to two-dimensional liquid chromatography (2D-LC)-mass spectrometry (MS)-MS analyses. The abundances of proteins in the axon are found to be strongly correlated with their average abundances in whole neurons. Based upon these data, a quantitative description of the protein distribution among various subcellular structures in the axon has been generated. The proteins extracted from the axons and whole neurons are also subjected to stable isotope dimethyl labeling reaction and then to 2D-LC-MS/MS analysis. Proteins enriched in the axon compartment of rat cortical neurons are thus identified.