Although genetically modified glyphosate resistant soybeans with cp4-epsps gene have been widely planted all over the world, the proteomic characteristics of them are not very clear. In this study, the soybean seeds of a genetically modified (GM) soybean line H06-698 (H) with cp4-epsps gene and its non-transgenic counterpart Mengdou12 (M), which collected from different planting regions in two years, were analyzed with label-free proteomics technique.