Objective: In the early stages of embryonic development, cell commitment occurs by thousands of genes and proteins; nevertheless quantity of each protein is crucial. In the most simplified model of human CNS development, human embryonic stem cells (hESCs) could develop into the neural cells in vitro. Materials and Methods: In this study, quantitative proteomics of hESCs investigated during neural commitment and differentiation by 2D-DIGE coupled MS/MS. Results: we found that expression of 137 protein spots modulated during differentiation, of them 118 proteins could be identified using MALDI-TOF/TOF and LC MS/MS. Several proteins involved in mRNA processing, protein folding and actin related proteins down regulated whereas Peroxiredoxins (anti oxidative stress proteins), anti apoptosis proteins, cell structure and motility proteins were up regulated in neural progeny. Gene expression, cell death, replication and recombination pathways connected in a significant manner to the hESC specific proteins and neural associated proteins were involved in the cell death, cell maintenance and cancer pathways. Functional analysis figured up that suppression of MAGOHB protein in hESCs enhanced the neural differentiation and hindered other lineages development by unknown mechanisms. Also we found that BCAS2 expression is mandatory for stem cells pluripotency and its knock down promotes differentiation through p53 signaling pathway. Conclusion: Current study provides us comprehensive source of proteins that affect neurogenesis in vitro and shed light on protein networks with a unknown functions in neutralization.