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What To Do When The HPLC Runs Dry

Mar 21, 2022

Here’s a question that came in anonymously because they let their HPLC run dry and they are wondering what to do.

So what do you do if your HPLC runs dry?

How to prevent your HPLC from running dry

First statement:  Don’t let it run dry. Here’s a trick: you can set a minimum pressure on your HPLC pump.  You basically tell it to shut down when the pressure drops to a specified level.  So for example, if you normally run at 100 bar and the pressure drops to 5 bar, then the pump will shut down.  

Basically what that means is if it starts pumping air the system will shut down. 

So that is one piece of advice to not let air bubbles get into your system.

So let’s deal with the fact that it has already happened.

What to do when your HPLC runs dry

Here’s my first statement: Don’t freak out! Don’t worry about it, it is not as nearly as bad as you think.  People are out there saying, “Air in your column!  Your column is destroyed!  You just threw away a $500 column.”

NONSENSE! Your column is fine; the instrument is fine.

Now, I don’t want you to run your instrument for long periods of time when it is dry, because if the HPLC pump runs dry your piston will rub against the pump seal, and that will eventually wear out.  But that is a long term issue. 

But in the short term simply worry about getting liquid back into your instrument.

I would start with 100% acetonitrile or 100% methanol and pump all the air out of the lines. So, open the purge valve to remove all of the air bubbles. At that point you can switch to liquid and start pumping liquid through.

Once you pressurize the column the gasses will dissolve so they will disappear.  You will see bubbles coming out for a little while.  But once you hydrate that column again, the column is going to be fine.  

I know that people say that if a column dries out that the column is ruined.  I don’t believe that is true, in fact I have data to say that that is not true.

We actually lost a column under a GC for three years.  We found it three years later and put it back on; it pumped bubbles for a couple minutes and from that point on it was perfectly fine. 

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