Chromatography Forum

Hi all,
Can I apply column baking when the MS is joined to the GC and without venting the MS vacuum?
And how?

Hi Dr. Malik,

I think perhaps with the MS it is better to remove the column from the MSD and cap it and perform the bakeout, as usual, keeping the column in the injector Or by trimming the ends first.

1. Put the inlet into split mode.
2. Set the column flow to the normal operating value, or set the capillary column gas velocity to 30 cm/s.
3. Set the inlet split vent flow to 200 mL/min.
4. Purge the column with carrier flow for at least 15-30 minutes before heating the oven.
5. Set the source 25°C at normal operating temperature.
6. Set the inlet temperature to 300°C or 25°C above the normal operating temperature to bakeout contaminants from the inlet, mostly through the split vent.
7. Set the column oven 25°C above the GC method final oven temperature to bake contaminants from the column at a 10-15 degrees Celsius/minute ramp rate. Do not exceed the column manufacturer's maximum temperature limit.
8. Bakeout for 30 minutes at the program's maximum value or until the detector baseline is free of contamination peaks.

Short answer: yes.

The disadvantage is that, depending what you're baking off, it might get stuck in your MS. Therefore, if you don't want to disconnect the column, i suggest to heat your transfer line, MS source and quad(s) to their maximum temperature during the column baking.

Most importantly, make sure there are no leaks when you put everything at max temperatures (perform MS air/water check).

Short answer: yes.

The disadvantage is that, depending what you're baking off, it might get stuck in your MS. Therefore, if you don't want to disconnect the column, i suggest to heat your transfer line, MS source and quad(s) to their maximum temperature during the column baking.

Most importantly, make sure there are no leaks when you put everything at max temperatures (perform MS air/water check).

If you can use Hydrogen carrier gas while baking it will help keep the MS clean if anything bakes off the column, and will provide cleaning for the inlet as well.

If I haven't injected anything very dirty and I just want to bake out the column to remove any extra column bleed I often raise the oven temperature and put the MS into manual tune mode and monitor the masses that come off as column bleed. For a 5 phase column it is most often m/z 207. I watch this maximize then fall off until it is a lower steady value then I know any oxidized phase has been baked out, you can also monitor m/z 18 to see that any residual water is also baked completely out of the column. Often new columns will have water adsorbed into the phase that you want to remove before using them for analysis. Most new columns are low bleed and there is not enough when conditioning to foul up the MS source.

Short answer: yes.

The disadvantage is that, depending what you're baking off, it might get stuck in your MS. Therefore, if you don't want to disconnect the column, i suggest to heat your transfer line, MS source and quad(s) to their maximum temperature during the column baking.

Most importantly, make sure there are no leaks when you put everything at max temperatures (perform MS air/water check).

If you can use Hydrogen carrier gas while baking it will help keep the MS clean if anything bakes off the column, and will provide cleaning for the inlet as well.

If I haven't injected anything very dirty and I just want to bake out the column to remove any extra column bleed I often raise the oven temperature and put the MS into manual tune mode and monitor the masses that come off as column bleed. For a 5 phase column it is most often m/z 207. I watch this maximize then fall off until it is a lower steady value then I know any oxidized phase has been baked out, you can also monitor m/z 18 to see that any residual water is also baked completely out of the column. Often new columns will have water adsorbed into the phase that you want to remove before using them for analysis. Most new columns are low bleed and there is not enough when conditioning to foul up the MS source.

James, do you use hydrogen for baking on systems that are on helium? Like, as simple as disconnecting the helium supply and connecting a hydrogen tank/generator?

We don't have a single GC-MS that uses hydrogen. But it sounds promising to do this once in a while, if it's as easy as it sounds.

For example, for our waste water analysis of PAHs we have to replace the analytical column a bit too often (GC-MS/MS). Tailing hurts the separation of the critical pair (benz(b)-benz(k)) so much that a column often doesn't last a month. This is with a retention gap (LVI), inlet maintenance, column cutting, and a post-column backflush. Do you think that an overnight bake with hydrogen carrier could help extend the column lifetime? Can you use the system on helium the next evening?

Now, I believe the main cause is that we run Quechers food extracts for pesticides on the same system/column in between PAH analysis. A dedicated GC-MS/MS for PAHs is on the wishlist...

Sorry for stealing the topic but i think the OP has been answered (?)

I installed a two way valve where I have He on one in port and H2 on the other in port and the out port goes to the instrument. I can switch to H2 and set the oven to 250C for the weekend and let it clean the system.

Agilent is now selling a setup similar to that which bleeds H2 into the source for cleaning either during a run or at the end of a sequence. They call it the Self Cleaning Source. It is supposed to keep the source cleaner longer.

When you run H2 through a system that normally runs He, it can take a week of baking to bring the baseline back down to where it was on He, but if you then switch back to He, it will have the cleanest background you can imagine

I installed a two way valve where I have He on one in port and H2 on the other in port and the out port goes to the instrument. I can switch to H2 and set the oven to 250C for the weekend and let it clean the system.

Agilent is now selling a setup similar to that which bleeds H2 into the source for cleaning either during a run or at the end of a sequence. They call it the Self Cleaning Source. It is supposed to keep the source cleaner longer.

When you run H2 through a system that normally runs He, it can take a week of baking to bring the baseline back down to where it was on He, but if you then switch back to He, it will have the cleanest background you can imagine

The aim would be to decrease tailing of PAHs by baking overnight/weekend with H2, then switching back to He. This in addition to normal maintenance. We only work in MRM mode (7000C) so i guess the background is no issue for switching.

I'm hesitant to try it out. I don't know what to expect since it could surely remove some dirt that causes tailing, but at the same time expose active sites that were deactivated by other dirt. It could go both ways...?

I did not realize I could clean up my column as well as my source. I'm going to add this to my maintenance routine.

It is definitely possible to get the source "too clean." When this occurs you'll see a climbing response over a few injections, and then it usually settles out after the active sites have gotten covered back up.

I've worked with lots of H2 carrier GCMS and observed the higher initial noise followed by a nice clean system many times.. I've also used JetClean quite a bit and like it a lot. Setup takes more work than you would think but there are some good guides available. Take a look at this user manual: https://www.agilent.com/cs/library/user ... Manual.pdf

And this application note: https://www.agilent.com/cs/library/appl ... 7254EN.pdf

JetClean was actually originally developed specifically for PAHs. It improves response stability greatly. Especially when you combine it with a 6 mm draw out lens / extractor lens (depending on source type.)

Running at a hotter ion source temp is recommended as well.

Lastly.. if you've got a 7000C: increase your collision energies. The PAHs are so stable they go through no problem, but any other matrix will get torn apart. I've gone up to 50 V with great results.

As far as the original question goes: as long as the column is flushed with lots of inert, clean gas before you heat it you are totally fine baking it out into the MS. Using the MS as a leak detector to avoid ever heating the column with oxygen in it WAY outweighs any downsides. Columns go through a lot of QC tests and one of them is to check bleed on an FID, you can check the paperwork that comes with the column to confirm. The column should be very low bleed by the time it gets to you, so just let it sit for a for a couple hours flushing with gas before baking it out, do an air/water check and if you are air free go ahead and increase it to the conditioning temp.

Hello,

I know this is a bit off topic from the original post but I am interested in the discussion of JetClean here.

My lab recently purchased an Agilent 8890/5977B GCMS that was set up with the JetClean module. However, I have been very disappointed with JetClean so far, as it does not seem to be cleaning the source sufficiently.

I have been running a "clean only" method after each sequence, but abundance still falls over a fairly short period of time (3-4 weeks). I have been using the manufacturer's settings, however, I let the cleaning process go for about 7 minutes instead of just 1.3. We do run pretty dirty environmental matrices but I have had to clean the source just as regularly as my other instruments, so far, so I was expecting a bit more from JetClean.

This process is very new to me (as is working with H2) so does anyone have any suggestions for parameters to change and make this work a bit better? Higher emission energy? More H2 flow into MS?

Thanks