Quantitative Proteomics of Nervous System Regeneration: From Sample Preparation to Functional Data Analyses

Mammals have a limited regenerative capacity, especially of the central nervous system. Consequently, any traumatic injury or neurodegenerative disease results in irreversible damage. An important approach to finding strategies to promote regeneration in mammals has been the study of regenerative organisms like Xenopus, the axolotl, and teleost fish. High-throughput technologies like RNA-Seq and quantitative proteomics are starting to provide valuable insight into the molecular mechanisms that drive nervous system regeneration in these organisms. In this chapter, we present a detailed protocol for performing iTRAQ proteomics that can be applied to the analysis of nervous system samples, using Xenopus laevis as an example. The quantitative proteomics protocol and directions for performing functional enrichment data analyses of gene lists (e.g., differentially abundant proteins from a proteomic study, or any type of high-throughput analysis) are aimed at the general bench biologist and do not require previous programming knowledge.