What is the best way to flush a liquid chromatography system to remove contamination?

For research use only. Not for use in diagnostic procedures.

Answer

Usually, contaminants that cause high background or produce a positive signal in a blank are hydrophobic chemicals. These compounds have high retention times on reversed phase (C18) columns. 

Contamination of a liquid chromatography (LC) system usually requires flushing the system with an organic solvent to remove unwanted background. Isopropanol (IPA) is the solvent of choice for flushing such contaminants out of an LC system. It is good at solvating organic molecules and is safe on LC hardware and tubing.

To flush the entire LC system to remove contaminants, follow these steps:
1) Place both pump inlets (A and B) into a bottle of IPA (500–1000 mL). Remove the LC column and place the LC line into a waste container.
2) Set the flow rate to 0.200 mL/min at 50% for each pump or 0.100 mL/min per pump. Let the pumps run for 12–16 hr (overnight). This will allow the LC system to soak in the IP, giving the contamination time to loosen up and dissolve, in case it is absorbed and retained on LC surfaces.
3) Increase the flow rate to 0.400 mL/min for each pump and let the pumps run for 30 min.
4) If the contamination is very hydrophobic, use other organic solvents such as a mixture of acetonitrile, acetone and isopropanol (1:1:1).
5) If the contamination is water soluble (inorganic), use a mixture of water and methanol (or IPA) (1:1). Alternate between flushing with water and flushing with IPA.

Note: If you want to use other solvents besides IPA, please make sure to consult SCIEX Tech Support to make sure no damage will be done to the system.