Dear Nrusingh,

Please find the attachment hopefully help.

Best regards

Aly

If there was just one peak, I would say it was a gradient peak.  But it is ongoing so I would say it is your pump B.  Calibrate as per the manufacturer's directions, then schedule a 'service call'.

In addition of the nice comments above, Have you tried blank injection? I mean just inject solvent of your compound. Have you washed your column with the mobile phase, if yes, did you get good base line? Are your compound pure? Do you have evaluated the stability of your compound in the solvent and mobile phase? Maybe it could help you to evaluate why you have many negative peaks, With best regards

Air bubbles in the PDA flow cell can cause the periodic negative peaks like you are observing especially during parts of the gradient where an organic solvent is being mixed into an aqueous mobile phase. Degas your solvents and/or check the performance of your vacuum degasser. A back pressure on the PDA flow cell might also help. You have to be careful how you do this because too much backpressure can rupture the flow cell. Check the manufacturers recommendations on the allowable back pressure on the PDA detector. The easiest way to increase the backpressure on the flow cell is to either decrease the diameter or increase the length of the tubing after the detector (flow cell). Connect the tubing directly to the HPLC pump outlet to evaluate the back pressure it generates. 

In addition of the nice comments above, have you checked the back pressure? In general, the back pressure should less than 1bar during the same MP composition. If the back pressure is unstable,  purge the system to remove the any air bubble.

Thank you all for your suggestions. It seems the Flow cell is generating back pressure. I am going to change the flow cell next week.

It may be an air bubble in the flow cell.  Take the column offline, they purge the HPLC with 100% Methanol at a 'high' flow rate (~5 mL/minute).