Dental stem cells isolated from oral tissues have been shown to provide with high proliferation ability and multi-lineage differentiation potential. Although the dental stem cells possess the potential of nerve regeneration, the specific expression profile of dental pulp stem cells (DPSCs) and periodontal ligament stem cells (PDLSCs) are still unclear. Here, DPSCs and PDLSCs, collected from the same tooth with 3 donors, were tested for high-throughput protein profiles by combining two-dimensional gel proteomics and TMT-based proteomics.