Anion exchange chromatography can be used in different ways. You can elute a compound of interest by changing the pH so that the analyte of interest is no longer charged (what you are asking about) or use gradients of concentrated anions. Doing it with pH will be difficult for you. First, I assume that you are looking at the free GAGs and not those attached to proteins. Heparin/heparin sulfate glycosaminoglycans, chondroitin/dermatan sulfate GAGs and keratin sulfate all have sulfate groups on them. That means that you would need to go well below pH =0 to put enough charge on the amide nitrogen (usually considered to be neutral). At these pH values, you will hydrolyze the GAGs.  Hyaluronans, which are non-sulfated, technically have an isoelectric point of about 1.2.

You can still use HiTrap Q to purify proteoglycans. For example [Proteoglycan]…”was further purified by applying to a HiTrap Q anion-exchange column (GE Healthcare) and eluting with a gradient of 0–2 M NaCl in 20 mM Tris/HCl, pH 8.0, and 0.2% CHAPS.” (See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359141/) Or http://link.springer.com/article/10.1007/s00441-003-0714-4#page-1 Or http://www.jbc.org/content/279/13/12511.full.pdf+html. You should be able to find many other examples by searching scholar.google.com.

Thank You 

I did thiolation for the sulphate group on unfractionated Heparin using HOBT/EDC/Cysteamine and I'm trying to purify the samples using PD-10 column. What are the buffers used for binding and elution in the column. Any Ideas ??

You can use phosphate buffer at PH close to 3.5. The glycosaminoglycan possess best negative charge and binding activity at this pH. You can use acetate buffer too if you want but phosphate buffer are much better.