CRL MS Facility Protocol: Cleaning the sample cone Cleaning the sample cone This may be necessary due to lack of sensitivity or fluctuating peak intensity, or if deposited material is visible on the outside of the sample cone. Please note that this procedure should only be attempted after the process has already been shown to you by a member of the MS Staff. If you have not been given this guidance please see a member of the facility staff before following this procedure. Proceed as follows: On the MassLynx top‐level window, launch the tune page. 
Select Standby. 
Switch off LC pumps. 
Disconnect the liquid flow at the rear of ESI probe. 
Set Source Temp to 20°C and switch off the heaters. Warning: Removal of the APcI probe or desolvation nozzle when hot may cause burns. Wait for 1 hour to let the system cool. Caution: Removal of the APcI probe when hot will shorten the probe heater's life. Tip: The cooling time will be significantly shortened if the API gases are left flowing. Warning: To avoid contamination with toxic and biohazardous materials, wear rubber gloves at all times while handling all source components. When Probe Temp and Desolvation Temp has cooled below 100°C: Switch off the nitrogen supply. Disconnect both gas lines from the front panel by undoing the source thumb nuts (See Figure 1). 1
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CRL MS Facility Protocol: Cleaning the sample cone Figure 1: Unscrew souce thumb nuts. Disconnect both electrical connections by pulling back on the plug sleeves to release the plugs from the sockets on the front panel. Undo the two knurled thumb nuts that retain the probe and withdraw it from the source. Place it carefully to one side. Undo the three thumb screws and withdraw the probe adjustment flange and glass tube. Place the glass tube on a flat surface and place the probe adjustment flange on top of the glass tube. Warning: When the source enclosure has been removed the source block is exposed. Ensure that the source block heater has cooled before proceeding. The sample cone is now accessible (See Figure 2). 3
CRL MS Facility Protocol: Cleaning the sample cone Figure 2: Sampe cone is exposed. Caution: The sample cone is very fragile extreme care should be given to ensuring the orifice is not damaged. Never place the sample cone on its tip, always place it on its flanged base. Figure 3: Exploding diagram for cone assembly It is not necessary to vent the instrument to remove the sample cone. The source block incorporates an isolation valve for this purpose. To remove the sample cone, proceed as follows: CRL MS Facility Protocol: Cleaning the sample cone 
Using a suitable flat blade screwdriver rotate the valve by 90° into its fully anticlockwise position (See figure 2 for position of valve). 
Disconnect the cone gas inlet line. 
Remove the two sample cone retaining screws using a 1.5mm Allen key and withdraw the sample cone and cone gas nozzle from the ion block. 
If necessary use a glass‐fibre pen to remove gross contamination from the cone gas cone surface by gentle abrasion. 
If the sample cone contains debris, place a drop of formic acid on the orifice. 
Immerse the sample cone and cone gas cone in separate glass vessels containing methanol:water (1:1). Do not place other metal objects in with these cones to prevent damage to the cone orifice. Note: If the parts are severely contaminated, use a mixture of 45% methanol, 45% water, and 10% formic acid. 
Place both vessels in an ultrasonic bath for 30 minutes. 
If formic acid was used in the cleaning solution: a. Rinse the parts by immersing them in separate glass vessels containing water and placing the vessels in the ultrasonic bath for 20 minutes, to remove the formic acid. b. Displace the water by immersing the parts in separate glass vessels containing methanol and placing the vessels in the ultrasonic bath for 10 minutes. 
Carefully remove the parts from the vessels and blow‐dry them using inert, oil‐free gas. Alternatively, the parts may be placed on lint‐free towels and allowed to air dry. Wipe off any water spots with a lint‐free cloth. Refitting the sample cone required a direct reversal of the removal procedure. Note: If you have any problems or are not sure about what you are doing then contact a member of the MS staff for help. 4