I'm trying to separate free chondroitin sulphate (CS) and keratan sulphate chains from bovine cartilage. After extraction with guanidine HCL, CsCl gradient density centrifugation was used to separate the aggrecan monomers (A1D1). Then I did b-elimination with 0.4M/0.5M NaOH with NaBH4 at lease 24hours and neutralized the pH with HCl. After desalted with 1kDa pore dialysis tubing, the sample was loaded onto DEAE ion-exchange column, eluted with 0.1-3M linear gradient NaCl.

But I found after b-elimination, the CS can't be detected by the CS antibody, can anybody share the potential causes please?