Retinal organoids have become valuable 3D model for translational and developmental research. The knowledge of the limitations of the system ensures its sensible use. All retinal cell types originate from the differentiation of retinal progenitor cells. The properties of retinal progenitors in 3D culture systems are not well studied. In our project, we created a mouse stem cell line with a Rax-mCherry reporter construct that allows retinal progenitors' isolation, tracing, and in vitro imaging during retinogenesis. For proteomic analysis, we used mCherry-positive cells from dissociated embryoid bodies with formed eye field structures on the fourth day after stem cell aggregation. Information about protein content helped to characterize Rax-expressing cells at this stage and their suitability for further applications.