Abstract: The present invention relates to a method for the purification, concentration and identification of glycosylphosphatidylinositol anchored proteins (GPI-APs) from a biological sample (cells, tissues and/or blood/serum) in a patient or subject, including a human patient or subject. A new method to separate GPI-anchored glycoproteins, a class of glycoproteins found in all animal cells and fluids including serum, from other glycoproteins and proteins for the purpose of identifying potential biomarkers for various diseases, including cancer, especially breast cancer, vaginal cancer, endometrial cancer, uterine cancer, cervical cancer, pancreatic cancer and prostate cancer. The method uses the alpha-toxin from Clostridium septicum to separate GPI-anchored glycoproteins for identification and optionally quantification. The GPI-APs so obtained may be used to raise antibodies for inclusion in an immunosorbent assay for the diagnosis or the monitoring of therapy of cancer in a patient.