I have tried using a eluent 100-150 mM NaNO3 in 100 mM NaOH after the treatment of the sample with 2 M NaOH, but the result is inconsistent. Sometimes there is no peak and quite often peak is shifted. Again in case of consistent retention time, inconsistency occurs in peak height and area considering the concentration. Please help me out.
Never tried. What is the NaOH (2M) doing ?? ... and what are you actually trying to analyse - presumably not the intact polysaccharide.
You might want to use sodium acetate rather the NaNO3. I asked Dionex once why they don't suggest other pusher ions and the answer was because they don't have enough data to know how to do the re-equilibration of the column (and that might explain your problems with inconsistent retention times). If you need a stronger pusher than the sodium acetate we once used sodium trifluoroacetate - that was very effective and gave nice sharp signals. We re-equilibrated the column in much the same way as we do normally and it didn't seem to be an issue.
By the way how are you re-equilibrating at the end of your run ? If you are using a PA1 I would recommend re-equilibration of at least 15 min ..... maybe longer.
Cannot suggest much more without more information
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