The results of LTQ Orbitrap LC-MS/MS mass spectrometry analysis of prostate cancer cell surface TF-Ag proteome presented in this study demonstrate that many of TF-Ag expressing cell surface glycoproteins in prostate cancer cells are in fact either well known stem cell markers (CD44, α2 integrin, β1 integrin, CD49f, CD59) or the proteins controlling important cancer stem-like cell functions (EphA2, CD138, transferrin receptor, profilin). This evidence concerns the gene CD59 and Familial prostate cancer.