Asma Foufou I think your should not have a problem separating the sugars with an NH2 column. So I have a few other points for you to consider:
Ensure that the SOP you are using does not lead to over-hydrolysis of your sugar compounds. The NREL laboratory protocol for sugar determination in biomass uses 4% H2SO4 for one hour at 121 degrees Centigrade to break poly-saccharides into monomer units. With high concentration H2SO4 at 100 degrees C you may see too much degradation and lose your sugars.
Also, ensure that the neutralization agent does not chelate with your sugar unit.
Lastly, run a method with a longer detection window OR observe your live window during the hour after injection to determine if this is a retention time issue. If you see compounds that are retaining too long for your detection time then consider adjusting the ratios of the eluent.