Glycosphingolipids (GSLs) are membrane lipids involved in numerous cellular processes and can be linked to diseases. With the aim to study the relevance of GSLs on early mammalian development, we generated glucosylceramide synthase-deficient human induced pluripotent stem cell lines (UGCG KO hiPSC). Thereby GlcCer-based GSL synthesis is completely abrogated. The UGCG KO hiPSCs maintained pluripotency as evidenced by teratoma formation in vivo. Here we compared whole cell proteomes of explanted teratoma derived from wildtype (WT) and glucosylceramide synthase-deficient (UCGG KO) hiPSCs by mass-spectrometry-based quantitative proteomics. Differential protein expressions of proteins related to pathways associated with signal transduction and protein localization were observed.