Abstract： Objective To analyze differences between CD133+ and CD133- glioma U87 cells by methods of proteomics.Methods 2D - PAGE was performed to separate the proteins of the CD133 + and CD133 - U87 cells,which were isolated by magnetic cell sorting.The differential protein spots were analyzed by software analysis,subject to in- gel digestion,and identified by matrix assistant laser desorption time -of - flight mass spectrometry ( MALDI - TOF - MS) and MALDI - TOF/TOF - MS.Results There were 73 differentially expressed protein spots observed in comparing between CD133 + and CD133- U87 cells by 2D -PAGE ( P ＜ 0.05 ).Spots with ＞ 1.5 - fold expression changes were 46,and ＞ 2 - fold were 27,and ＞ 3 -fold were 8.Ten spots were increased,while 63 spots were decreased in CD133 + U87 cells.Forty -four high -quality peptide mass fingerprinting and 35 proteins were obtained by MS. Conclusions There are significant differences between CD133+ and CD133- U87 cells.Differentially proteins have been obtained by proteomics analysis,which are important targets to the study of brain cancer stem cells (BTSCs).