Liquid Chromatography Blog

Does Air Damage My Column?

Q: I accidentally ran out of solvent in an overnight run on my HPLC system. I had not activated the low-pressure limit on the pump, so the pump just pumped air for half the night. Will this ruin my column? If not, how can I get all the air out?

First of all, you’ve made an assumption that is not true. If the reservoir runs dry, you will indeed draw air into the pump, but the pump will not pump air through the system. HPLC pumps are designed to pump liquid, not air. When they fill with air, they lose their prime and stop pumping. Yes, you may pump a few bubbles of air into the column before the pump quits entirely, but the pump will not have pumped air through the column all night. And even if it had, it is unlikely to have caused problems.

HPLC Solutions #8: Does Air Damage My Column? Figure 1

   To correct the problem, you will need to first re-prime the pump by purging the air from all the lines. I would remove the column before starting. Start by degassing the solvent thoroughly. If you use an in-line degasser, this may be sufficient, otherwise I recommend helium sparging. Then open the purge valve at the pump outlet and prime the pump in the normal manner. With some pumps, this will mean filling the tubing between the reservoir(s) and pump with the aid of a syringe. Run the pump for several minutes at high flow (e.g., 10 mL/min) to clear all the air from the pump and connecting tubing. Then turn the flow rate down to 1 mL/min or so and close the purge valve to clear the tubing to the inlet of the column until no more bubbles emerge. Before shutting off the pump, switch to 100% methanol (MeOH) or acetonitrile (ACN) – because of their low viscosity these solvents will help to remove any air bubbles from the column.

   The next step is to clear any air from the column. Re-connect the column inlet, but do not connect the column to the detector. If you want a visual aid to your progress, attach a piece of connecting tubing to the column outlet and place the free end in the bottom of a beaker or other waste container. Start the pump and increase the flow to generate 3000-4000 psi (200-275 bar) of pressure (the increased pressure will help to compress bubbles back into solution so that they can be removed more easily). Run the pump for 10 min or so, or until no more bubbles emerge from the waste line at the end of the column. Turn off the pump, reconnect the detector, and you should be back in business. There may be a few air bubbles in the detector, but these should clear quickly in a minute or two.

   I have described the procedure for purging air from a reversed-phase column. If you are using another chromatographic mode, other solvents may be appropriate. If you are not using a silica-based column, be careful not to exceed the recommended maximum column pressure. You can follow this same column purging procedure if you inadvertently leave the end plugs off the column and get a little air in the ends for the column during storage.

   One side effect of running the pump dry for an extended period may be damage to the pump seals. The mobile phase acts as a lubricant between the piston and pump seal as the piston moves back and forth. Without this lubrication, the pump seal may be damaged. During the column purging procedure discussed above, check for any leakage out the drain hole below and behind the check valves. Leakage is a sign of pump seal damage. If no leaks are observed, return the pump to normal operating conditions and check the pressure. If the pressure is steady and normal, the pump should be OK. If the pressure pulses, especially for one pump head in a two-pump system, the seals may be damaged. If any signs of pump seal damage are present, the seals should be replaced. Alternatively, as a safety measure or if the pump seals are nearing their replacement interval anyway, replace the pump seals before purging the system and you will not have to worry about them.

This blog article series is produced in collaboration with John Dolan, best known as one of the world’s foremost HPLC troubleshooting authorities. He is also known for his ongoing research with Lloyd Snyder, resulting in more than 100 technical publications and three books. If you have any questions about this article send them to


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