Thank you for your answer.

I 'm giving you more detail. I use Triethylammonium Acetate buffer (pH around 8) and my compound is an oligonucleotide (negatively charged due to the phosphate link) coupled with a glycocluster (positively charged). 

The TEAAc buffer is our ion-binding reagents for our negatively charged compounds. But since i try to synthesize compound with both charge, i encounter some difficulties to purify them.

You coud also try to heat the column during chromatography, or "melt" the sample at 90 °C in an eppendorf vial, then freeze it in liquid nitrogen and inject the sample immediately when liqufied again.

Dear,

Your provide information in the question is insufficient to answer exactly. However up to an extent where i got your question is that check the pipelines connecting the detector. Sample preparation and pipetting may also be one of the issue to be taken under consideration. pH is one of the important factor and the ion pairing agent compatibility with your analytes also need s to be evaluated. I was also having some secondary structures attached to the peaks of the original analytes, and i came to know very later that my analytes were degraded (oxidation) and i need to take fresh analytes from market.

Thank you both.

I have an oven on my hplc so i try at different temperature (30°C and 70°C), and nothing change. Maybe i can try to "melt" directly my samples but i think the temperature decrease quickly when i inject my samples.

My analytes were freshly made and i control them with a MALDI-Tof, so i don't think there is any degradation. I have no problem of purification with other samples (without cation), so i don't think the preparation or pipetting has any influence on the analysis.

Thank you for your help.