Human embryonic stem cells (hESC) are being exploited for potential use in cell transplantation due to their capacity for self-renewal and pluripotency. Dopamine (DA) neurons derived from hESC represent a promising source of cell replacement therapy for Parkinson's disease (PD). While gene expression on the transcriptome level has been extensively studied, limited information is available for the proteome-level changes associated with DA neuron differentiation. Here we analyzed the proteome of differentiating DA neurons to search for the potential biomarkers to assess the efficiency of differentiation. Although the proteome profile of DA neurons did not exhibit significant changes, a number of cytoskeletal proteins including nuclear lamin, tropomyosin 1, and myosin light chain 1 were specifically up-regulated during differentiation. Expression analysis of the respective genes was also consistent with the proteome results. In addition, these differentially expressed proteins form protein interaction network with several PD-related proteins suggesting that they may play roles in PD pathogenesis as well as the maturation of DA neurons.