We usually open the instrument when we need to perform maintenance on it (changing filaments, cleaning ion source, etc). We try to do this as infrequently as possible because it takes at least a day for the instrument to equilibrate (it’s also a lot of work as you can see below).

HPChem

Agilent

HPChem

Preparation

1. Go to Instrument Control > View > Diagnostics & Vacuum Control.
2. From here, go to ‘Vacuum’ > ‘Vent’. Wait for venting to complete.

The screen will tell you to turn off the oven and MS. Turn off the oven and detector by pressing the buttons on the GC. Do not turn off the injector port; doing so makes venting the instrument take longer.

3. When the screen says Vent Cycle Complete turn off the MS using the power switch in the back.
4. Unplug the vacuum pump from the outlet.
5. Prepare tools and replacement filaments for the instrument.

There are two types of filaments used for the instruments. Make sure you use the correct one when replacing the filaments.

Opening the Instrument

6. Remove the cover from the MS and unplug/unscrew the cables attached to the top unit.
7. Unscrew the clasp between the GC/MS.
8. Open the GC door so you can see inside the oven. Using your left hand, hold the long part extending from the GC. Using your right hand, grip the bottom of the MS. Carefully separate the two parts, checking inside the oven to make sure the column doesn’t get damaged. There may be some resistance from the vacuum seal, so work slowly and carefully until you hear a “pop” sound.
9. Once the seal is broken, pull the MS out until the long part is fully visible. Lay down some scratch paper (clean side up) on the table and place the MS cover on top.
10. Lift the top unit from the MS and gently place it down on the table so it lays on the paper and is shielded by the MS cover (flat side down, cables facing up). Cover the MS with a vial box or a MS cover from another instrument.

Sometimes the rubber seal will also come off when removing the top unit. Try not to remove it if possible, but if it lifts up, use a Kim wipe and methanol to clean the seal.

Removing the Ion Source

The screwdrivers you need to remove the parts are in a box along with the materials used to clean the ion source.

I recommend you wait a few minutes for the parts to cool down before proceeding because the parts are hot and will burn you if you’re impatient.

11. Unplug the cables from the front and side. You can either take a picture of the cables or follow the labels later when reattaching cables.
12. Unscrew the yellow part by slotting the larger screwdriver into the holes and turning counterclockwise. Do not touch the surface of the unit with the screwdriver.
13. Unscrew the top and bottom screws with the smaller screwdriver. Do not unscrew the other two screws yet; those hold the filaments in place on the ion source.
14. Slowly remove the ion source from the instrument.

You can use the larger screwdriver as a lever if it’s not coming out, but don’t use too much force or else you’ll damage the ion source.

15. Remove the screws from the filaments and disassemble the ion source for cleaning (if needed).

You don’t need to disassemble the source if you’re only replacing the filaments.

Cleaning the Ion Source

You can skip this entire section if you’re only changing the filaments.

16. Lay down some scratch paper (clean side up) and grab the following supplies from the same drawer you got the screwdrivers from:

• aluminum oxide
• cotton-tipped applicators (super long Q-tips)
• methanol vial(s)
• (for later) aluminum box (it’s a little rectangle folded from aluminum foil used for baking later)

17. Dump out a small amount of aluminum oxide on the paper.
18. Dip the cotton-tipped applicators in methanol, then a small amount of aluminum oxide and vigorously scrub at the tarnish on the ion source parts until they look clean. Repeat until all parts are clean.

Cleaning the parts that make direct contact is more important than cleaning the exterior parts. When cleaning the repeller, spend extra time cleaning the round part. If you try to clean the rest of the repeller, you’re gonna be there for a long time.

19. Thoroughly rinse all the parts under water (sink water is fine, doesn’t have to be DI water). Place the parts in a jar of methanol and sonicate it for ~20 minutes.

The sonicator is in the second-to-last room at the far end of the main lab. Don’t leave the sonicator on for too long because people complain that it gives them a headache.

20. Get a second jar, decant/dispose the methanol, and clean the bottom of the jar with a paper towel. Fill the jar with clean methanol.
21. After sonicating, use tweezers (top drawer, same cabinet as the other stuff) to transfer the parts to the second jar and shake it a few times.

We do this to make sure there’s no residual aluminum oxide from sonicating.

22. Transfer the parts from the second jar to the aluminum box, then bake the parts for ~30 minutes at ~100°C.

You can use the oven or any instrument that’s not currently in use.

Reassembling the Ion Source

Let the parts cool down before reassembling. [insert pictures here]

Reassembling the Instrument

23. Place the ion source back into the top unit, making sure all parts fit together snugly. Reinsert the top and bottom screws holding the ion source in place.
24. Replug the cables into the correct spots.
25. Clean the surface of the top unit with a small amount of methanol on a Kim wipe to remove contaminants.
26. Clean the rubber seal with a small amount of methanol on a Kim wipe to remove dust. Also check that the seal is firmly seated.
27. Slowly lift the top unit and reseat it on the MS. Make sure that the top unit is firmly in place and that it doesn’t wiggle.
28. Reconnect the MS to the GC by refitting the long part to the top unit. Try to leave a bit of space so we have room to reattach the clasp.
29. Reattach the clasp holding the seal between the GC/MS.

Restarting the GC/MS

30. Plug the vacuum pump back in and let it run for ~5 minutes.
31. Turn on the MS using the switch in the back.
32. Go to Vacuum > Pump Down on the computer. Wait for the instrument to pump down.

The pressure should start around ~150 or so and go lower from here. If it’s really high (~4000-6000) that means there’s a leak somewhere and you need to vent the instrument and troubleshoot.

Agilent

Preparation

1. Go to Instrument Control > View > Tune and Vacuum Control.
2. From here, go to ‘Vacuum’ > ‘Vent’. Wait for venting to complete.

The screen will tell you to turn off the oven and MS. Turn off the oven and detector by pressing the buttons on the GC. Do not turn off the injector port; doing so makes venting the instrument take longer.

3. When the screen says Vent Cycle Complete turn off the MS using the power switch at the bottom.
4. Unplug the vacuum pump from the outlet.
5. Prepare tools and replacement filaments for the instrument.

Opening the Instrument

6. Remove the front cover from the MS and unscrew the valve to release the vacuum seal.
7. Release the lever on the top of the MS to open the cover for the ion source.
8. Pull the side board open to expose the unit.
9. Unplug the cables connected to the ion source.

I recommend you take a picture beforehand because it looks like a tentacle monster.

10. Remove the screws holding the ion source in place.

Cleaning the Ion Source

Same process as detailed above.

Reassembling the Ion Source

Let the parts cool down before reassembling. [insert pictures here]

Restarting the GC/MS

11. Reinsert the ion source into the unit, then reconnect all cables. Make sure you reconnect all the cables and that they’re connected in the right order, otherwise you’ll get errors when trying to pump down later.
12. Close the side unit (making sure it’s pressed down tightly) then reconnect the vacuum pump. Hold the side unit in place until the vacuum seal is holding it in place. Alternatively, you can screw the side piece in to hold the side unit in place if there’s nobody around to help you with reconnecting the vacuum pump. Let the vacuum pump run for ~5 minutes.
13. Turn on the MS using the power switch at the bottom.
14. Go to Vacuum > Pump Down. Wait for the instrument to pump down.

If the computer is throwing up errors at this point, you either forgot to connect a cable or the cables were connected in the wrong order. Vent the instrument and check the connections. If all connections are correct, it is possible that one of the circuits in the board is burnt out and needs replacing. Ask Robert for help if that happens.