Removing a Clog from a Flow Cell

This Information Applies To: Agilent UV and RID detectors

Issue

A clogged flow cell causes high backpressure. The clog can be removed by flushing the system with solvents at high pressure. If you suspect a clog or experience high backpressure due to the flow cell follow the procedure below.

 Steps to follow 

Before proceeding:

1. Disconnect the column and replace with a union. 

   Caution: If the column is left in the flow path, it may be damaged during the flushing procedure.

2. Reverse the flow cell inlet and outlet lines. The clog is most likely closer to the inlet and therefore will have shorter distance to travel in removing it.
3. If there are multiple detectors in series, disconnect all but one detector. Perform the clog removal and flush steps for each separate flow cell.
   This precaution is needed to set the correct pressure limit for each detector. 
   
4. Set the maximum pressure limit according to the flow cell backpressure limitation reported in its manual.   

Steps to follow for reversed phase application:

• Clog removal

1. Open the purge valve and set the flow rate of 5 mL/min for each channel with HPLC grade water. Some pumps will require to manually open the purge valve and in others it is done via the software.
   During step 1, check that the solvent is freely moving through the solvent lines. If tiny air bubbles are observed in the lines continuously, it’s probably due to clogged solvent filters. To test, you can remove the solvent filter and if the bubbles no longer appear, replace the filter.
2. Close the purge valve and set the flow rate at 0.2 mL/min and flush the system.
3. Monitor the pressure. It will slowly rise, then either:
   1. The pressure will drop drastically, indicating that the clog was removed,
   2. The pump will shut down when the maximum pressure limit is reached, indicating the clog has not been removed.
4. If the clog has not been removed, let the system sit for at about 10 minutes until the pressure decreases. 
5. Repeat steps 2–4 up to three times.

   Confirmation: If the clog was removed, and the pressure should be stable and no longer rising. You can proceed with the system flush, otherwise contact Agilent Technical Support.

• System flush

1. Flush the system for 1 hour, with HPLC grade water. Verify that the pressure does not exceed 60 bars for UV, and 7 bars for RID during this step. Adjust the flow not to exceed the pressure values indicated. If it is not possible to proceed, contact Agilent Technical Support.
2. Flush the system with 100% isopropanol (IPA) at 1 mL/min, for a minimum of 1 hour. Make sure that the pressure does not exceed 60 bars for UV, and 7 bars for RID during this step. If it is not possible to proceed, contact Agilent Technical Support.
3. Flush the system with water at 1 ml/min, for 1 hour to remove the IPA.
4. Flush with your mobile phase as per your method settings for about 20 minutes, until the pressure is stable.
5. Reconnect the column and equilibrate the system. 

Steps to follow for normal phase application:

• Clog removal

1. Open the purge valve and set the flow rate of 5 mL/min for each channel with HPLC Isopropanol (IPA). Some pumps will require to manually open the purge valve and in others it’s done via the software.
   During step 1, check that the solvent is freely moving through the solvent lines. If tiny air bubbles are observed in the lines continuously, it’s probably due to clogged solvent filters. To test, you can remove the solvent filter and if the bubbles no longer appear, replace the filter.
2. Close the purge valve and set the flow rate at 0.2 mL/min to flush the system.
3. Monitor the pressure. It will slowly rise, then either:
   1. The pressure will drop drastically, indicating that the clog was removed,
   2. The pump will shut down when the maximum pressure limit is reached, indicating the clog has not been removed.
4. If the clog has not been removed, let the system sit for at about 10 minutes until the pressure decreases.
5. Repeat steps 2–4 up to three times.

   Confirmation: If the clog was removed, and the pressure should be stable and no longer rising. You can proceed with the system flush, otherwise contact Agilent Technical Support.

• System flush

1. Flush the system with HPLC-quality IPA with a flow rate of 1 mL/min for a minimum of 2 hours. Make sure that the pressure does not exceed 60 bars for UV, and 7 bars for RI, during this last step. Adjust the flow not to exceed the pressure values indicated. If it is not possible to proceed, contact Agilent Technical Support.
2. Flush with your mobile phase as per your method settings for about 20 minutes, until the pressure is stable.
3. Reconnect the column and equilibrate the system. 

Learn how to effectively troubleshoot your Agilent UV Detector: HPLC-0GEN-2201e - Chromatographic Troubleshooting for HPLC e-learning course available from Agilent education