Flushing the Calibrant System on your LC/MS System

Answer

This Information Applies To: Agilent LC/MS Systems

Issue

When there is suspected contamination of the CDS, low tune response, or possible blockage in the CDS, flushing the Calibrant system may be required.

Warning: This procedure risks exposure to hazardous, toxic, or flammable solvents and reagents. Wear appropriate Personal Protective Equipment as described in the material handling and safety data sheet supplied by the chemical vendor, and always follow good laboratory practice.

Items Required

• Clean powder-free gloves
• Ultrapure LC/MS Grade Acetonitrile
• Ultrapure LC/MS Grade Water
• Tuning solution (see the article What Tuning Mix do I Use to Autotune my Agilent LCMS System?)
  
  

Steps to Follow

1. Stop the LC/calibrant flow to the MS.

2. Disconnect sample tubing from the top of the nebulizer and place into a clean beaker or waste bottle.

3. Remove the CDS bottle and discard any old tune solution. See Figure 1.

4. Rinse the CDS bottle with LC/MS grade acetonitrile and then LC/MS grade water. See Figure 1.

   Tips: In the case of a highly contaminated bottle, the bottle can be cleaned with Alconox and hot water (60 to 70 °C), then rinsed as per step 4.

5. Flush the CDS with 50/50 (v/v) LC/MS grade acetonitrile and LC/MS grade water:

   1. Fill the rinsed CDS bottle with approximately 20 to 30mL of the acetonitrile/water mixture.

   2. Install the bottle and turn on the calibrant flow.

   3. Run the calibrant flush for at least 10 min.
      

      
      Figure 1. Removing and rinsing the calibrant bottle
      
      

6. Reattach the sample tubing to the top of the nebulizer.

7. Repeat step 5 with just LC/MS grade acetonitrile and flush for at least 10 min.

   Tips: To confirm cleaning procedures, you can monitor the MS spectrum and watch the contamination decrease over time.

8. Discard any remaining solvent and add fresh tune solution to the bottle. See the following articles on how to prepare the calibrant for your system:
   Filling the Calibrant Bottle in Agilent 6100 Series LC/MS Instruments
   Filling the Calibrant Bottle in Agilent 6200/6400/6500 Series LC/MS systems

9. Flush the fresh tune solution through the CDS for 5 min. Monitor tune ions to ensure that response is adequate.