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Agilent 6400 Series Triple Quadropole Mass Spectrometer

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6400 Series QQQ Vent and Clean Procedure (In Progress)

The instructions provided should be used to supplement the official 6000 Series LC/MS System Maintenance Guide. Go to Agilent.com, click on Resources on the menu near the top, select library and then user manuals. Search for 6400 Series LC/MS System Maintenance Guide.

What you will need:

Sonicator Bath

Di H2O                                                      

LCMS grade H20

LCMS grade Methanol

Clean glass beakers, various sizes from 200 to 1000 mL

Clean glass graduated cylinder, 100 mL

Liquidnox (www.alconox.com)

T8, T20, Torx screwdrivers

1.5mm ball screwdriver

Canted Spring Coils (2)

Ion Transfer Capillary

*These do not need to be replaced every vent and clean. Consult your service engineer or Agilent for the change intervals. The guide will include instructions on how to change the coils in the desolvation assembly and if replacing out the ion transfer capillary with a new one, you obviously do not need to clean it.

Ample space in front of the mass spec, behind the mass spec and ample table space to set parts on.

Ample time to perform the procedure (2-4 hours to perform, overnight to pump down).

Vent the system

Make sure you are not running any samples and there is no flow into the mass spectrometer. Using the Mass Hunter Data acquisition program, vent the system by right clicking within the QQQ Section and selecting vent.


When selected, a dialog box appears with the following message:


If you are sure you want to proceed, click yes. When the process is complete another dialog box appears:


It is now safe completely power off the instrument. Start by switching off the power button front cover of the mass spec.


Next, unplug the main power cable. The location is behind the mass spec and the main power cable is the lower left one. The cable is removed here.


Locate your vacuum foreline pump, switch off the power to the vacuum and then unplug it from the back of the Mass Spectrometer.


Next, grasp the handle on the front cover and pull it towards you.


Once it is angled toward you, pull straight up to remove it from the bottom.


The LED cable is still attached to the cover to the backside of the cover.


Release the cable by spreading tabs apart. The cable is now loose and can be removed.


Place the front cover somewhere out of the way. With the front cover out of the way, the next step is to remove the top cover.


There are two screws holding the top cover in place. Go around to the back and remove these screws.


Lift the top cover out and place it somewhere out of the way. Next, the left side cover near the source must be removed. To accomplish that, we must remove 4 screws. Use a Torx # 8 screwdriver to remove them. Also, remove the solvent line from the column compartment to the selection valve, if you haven’t already.


Life the cover and place it out of the way. Now, we are left with a few cables to disconnect and remove from the auxiliary module.


Remove the LED Cable from the display board slot, also remove the selector valve and leak sensor cables.


The spray chamber high voltage cable on the left side can be removed when the tab is pressed in.


Next loosen the  retaining screw on the bracket of the desolvation chamber. Then remove the nitrogen drying gas line and drying gas heater cable.


The drying gas heater cable can be removed by twisting it to release.


The drying gas line is removed by adjustable wrench, but the Source must be removed before you can have enough clearance to remove the line. Remove the line from your selector valve to your ESI needle first and then lift the source off the two pins on the door hinge. Img25.pngImg26.png

Set the Source off to the side.

Remove the main board 1 cable from the back of the auxiliary module. Lift the auxiliary module up and set aside.


Use a flat head screwdriver to loosen the drain hose tubing here and remove it.


Remove the sprays shield by turning counter clockwise and set to the side on aluminum foil. Use a Torx T-10 screwdriver to remove the two gold screws located on the front. Remove the face plate along with the middle piece and set to the side. Also, remove the capillary cap and set to the side.


Replace your gloves with fresh clean gloves, grasp the ion transfer capillary and pull it straight out. Pull straight out or risk breaking it as you remove. Set to the side on to aluminum sheet.


The desolvation assembly is removed next. Use a T-20 Torx screwdriver to remove the retaining screws at the upper left and lower right corner. Slide it out from the support rods. Place the desolvation assembly onto aluminum foil and prepare to change out the two canted spring coils.

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Use a needle nose plier to remove the two cables. Use a T20 Torx screwdriver to remove the 4 screws on the front.


Remove the front part of the desolvation assembly and make note of the orientation of the brown spacers covering the opening that holds the first canted spring coil.

Img 38.pngImg39.png

Remove and set to the side.


Use a fine pointed forceps to remove the coil from the holder. Place a new coil into the holder by pushing with your fingers into the channel within the holder. Avoid using tools to insert, as you may damage your new coil. Insert one side of the coil into the channel, hold it in place while you push the rest into the channel. It will expand and fit.


Next, go to the back side of the desolvation assembly, remove the four T-20 screws, pull the cover off and disconnect the two cables


Remove the 2nd canted coil spring using the forceps.


Place the new canted spring coil and push it into the channel to seat it.


Reconnect the 2 cables and place the cover back on the Desolvation Chamber. Tighten the 4 screws to secure. Reassemble the front of the chamber, place the spacers in the correct orientation secure with the 4 screws and install the two cables. Set the assembled chamber off to the side. Prepare to remove the ion optics.


Clean away any dust from the top of the manifold, loosen the two retaining screws on the right side and use a Torx-T20 screwdriver to remove the two screws on the left.


Lift the cover away and place somewhere safe. In the vacuum manifold, take a look at the cable connection arrangement of the ion optics. The green wire is plugged in on top and the black is plugged in the bottom. The Lens cable is connected through a plug style harness. Disconnect all three cables


The next step is to remove the ion optics. Use your right hand to push on the back of the skimmer spacer while on the front side, use your left hand to gently pull on the skimmer spacer. There will be some resistance until it suddenly will be loose enough to remove. Ensure that the ion optics does not bang or drop onto anything. Place the ion optics onto aluminum foil for further disassembly.

At this point, if you have an electron multiplier horn and wish to change it out, now is the time to do so. If not changing out the electronic multiplier horn, place the manifold cover back on to minimize dust.


Locate the electron multiplier horn on the right side of the manifold.


Disconnect the signal wire from the electron multiplier horn. Release the Multiplier from its cage by squeezing together the two hoops on the retaining clip, push down to clear the hooks and lift up to open.


Remove the electron multiplier horn and replace with a new one. Seat in the new multiplier.


Secure with the retailing clip and reconnect the signal wire. Now let’s go back to the previously removed ion optics assembly.

Remove the two screws on the front of the ion skimmer.


Grasp the edges of the skimmer with your left fingers, hold the assembly by the black spacer with the other and pull out the skimmer. Do not drop the skimmer.


Set the skimmer on flat surface, make sure nothing touches the center cone opening.


Rest the assembly on the spacer skimmer such that the lens 2 is facing up. Use a 1.5mm ball screwdriver to remove the two screws here.


Remove the Lens 2, set to the side. Remove the spacer insulator directly beneath. Then Remove Lens 1.


Remove the last spacer. Set all to the side.


Next remove these two screws that hold the octopole to the skimmer spacer. Hold onto the octopole tube while doing so, do not drop it.


Set the skimmer off to the side, disconnect the red and white wires on the octopole. Make note of the orientation before you remove.


The skimmer spacer is still tethered to the Octopole by the blue wire. Remove that screw using a torx screwdriver, remove the electrical harness and place the screw back in and tighten down so you don’t lose it. Leave the yellow wire connection to the skimmer spacer alone.


Let’s gather all the parts to go into the sonicator. Don’t forget the spray shield, face plate and capillary cap from before. Ensure that you do not sonicate any spacers or o-rings. If you did not replace the ion transfer capillary with a new one, then include it for cleaning.


Place two 1mL pipette tips on each end of the Ion transfer capillary. Use scissors to cut the end of each tip.


Place the ion transfer capillary into a glass graduated cylinder. Place the Ion sweep cone, ion transfer cap, face plate into a clean beaker. Place the Lens 1 and Lens 2 into a separate clean beaker. Finally, place the octopole assembly into a clean beaker.

Clean and sonicate parts.

(Handle each cleaning step with fresh gloves) Prepare a solution of 1% Liquidnox in deionized water or LCMS grade water. Fill each beaker to completely submerge all parts and sonicate for 10 - 15 mins. Do not sonicate for more longer than that. Discard the solution in each beaker and one by one, rinse off the solution from the parts with copious amount of tap water. Place all parts into new clean beakers and graduated cylinder. Fill each beaker with LCMS grade Isopropanol and sonicate for 5 mins. Remove the solvents from the beakers and fill up with LCMS grade Methanol. Proceed to sonicate for 5 mins again. Perform the previous step again to remove all traces of residue from each sonicated part.



To dry each part with house nitrogen gas, keep it submerged in the methanol until ready to completely dry with the nitrogen. Dry each part, one at a time and set onto clean aluminum foil. If house nitrogen is not available, place all parts onto aluminum foil and allow to air dry.

Re assemble the Ion Optics

Place the octopole onto the skimmer spacer. Hold in place and secure with the two screws.


Place the spacer back onto the end of the octopole assembly, then place lens 1 into the assembly by locating the correct hole that the pin will insert into.


Place the other spacer back onto the lens 1 then install the lens 2. Secure with the two screws.


Reconnect the white and red wires onto the octopole assembly. Screw the blue wire back on.


Install the O-ring to the back of the skimmer. Ensure that the skimmer spacer has its O-ring installed as well.


It is likely that the O-ring could still be stuck in the vacuum manifold. Try to keep it secure here or on the skimmer spacer while re-installing the ion optics assembly. You may need to try a few times to get it seated and seal properly.


Slide the ion optics back into the manifold. Re-connect the black and green wires as shown. Reconnect the electrical harness.


Place the manifold cover back on. Secure with two screws on the left side and tighten down the two screw on the right.


Next, reassemble the 3 pieces that will install to the front side of the desolvation assembly.


Align the face plate to the two holes here. Screw to secure but do not tighten all the way.


Instead, screw the spray shield in all the way, and once it is seated and connect screw in anymore, align the hole on the top of the spray shield to the 12 o’ clock position, hold that position and finally, tighten the two screws. Remove the spray shield and re-install spray shield to ensure that the hole on the front still lines up at the 12 o’ clock positon. Remove the spray and set to the side, for now.


Align the two guide posts onto the desolvation assembly. Slide the desolvation assembly to the end and secure with the two screws.


Lubricate the ion transfer capillary by spraying the sides with LCMS grade Isopropanol. Insert into the desolvation assembly. Go slowly and straight in. You will meet resistance at around this position.


Push the ion transfer capillary back even further, until you reach this position.


Place the ion transfer capillary cap back. Screw in the spray shield.


Align the auxiliary module up with the slot on the right side. Place the auxiliary module in position.


Reconnect the drain tubing on the bottom of the desolvation assembly, reconnect the nitrogen drying gas line and drying gas heater cable.


Insert cable into the main board, located on the back of the auxiliary module.


Reconnect the spray chamber high voltage cable, and tighten the retaining screw located on the bracket.


Replace the cover. Secure with the 4 screws. Reconnect the display board LED, selection valve and leak Sensor cables.


Place the Source back onto the two hinges on the door. Plug the line from selector valve back to the ESI probe. Place the line from the column compartment back into the mass spec.


Place the lower end of the mass spec front cover on. Attach the LED display cable. Push the front cover forward to secure it on the front the instrument.


Plug in the main power cord and the foreline pump power cord. Ensure everything is connect properly and correctly. Power on the switch on the back of the vacuum pump.


Finally Power on the Mass Spec. Allow roughly a full day to pump down the mass spec. You are finally finished.