Chromatography Forum

Dear there,
I am using an Agilent 6890/5973. Because I found N2 in autotuning and also peaks of dimethylpolysiloxane, i decided to change column. Yesterday, I changed pump oil first and the replaced a new DB-5MS column under the diretion of a Postdoc in our lab. He asked me to connect the two ends of the column to the inlet part and the MSD interface first, and then do conditioning. I realized now that this is absolutely wrong. However, it was operated like that. Before the conditioning, the gauge reading is 3.7*10 to -5 torr, close to what I usually have. But this morning (after conditioning), it is almost 9*10 to -5 torr. I tried to autotune, but tune stopped: cannot achieve constant peak widths.
I don't know if this is an air leak problem or the ion sources need to be cleaned. Why the vacuum got worse after the conditioning? What should I do first?
Thanks a lot. I know I did a stupid thing. Please help!

What do you mean by sayig " I found N2 in autotuning"?

Also what kind of conditioning are you referring at (i.e. what is the conditioning consists of)?

You may have a leak at the column connections - vespel-graphite ferrules bed in after a temperature programme and need to be re-tightened slightly.

If you opened the MS when you installed the column you might have a leak on the big O-ring that seals the side plate.

If you see only high nitrogen when you tune, and not extra oxygen and water you may have a leak in the helium supply line upstream of the gas purifier cartridge - air diffuses in through the leak and the gas purifier takes out the oxygen and water but leaves the nitrogen.

The moral of the story - read the instructions in the manual !

Peter

I did find m/z 28 in my tune report. Provided that m/z 32 is not observed at 1/3 the intensity of m/z 28, I guess there is no air leak in your MSD. However, I'm not sure where m/z 28 comes from and what it is.
For the MSD vacuum, I think there'd be nothing related to your column conditioning. MSD is set to protect itself from tuning when the vacuum rises to a certain value. Thus, please check if you are using a very high column flow rate;or is there any significant air leak in your MSD that makes the pressure increases? Try to re-tighten the MSD column nut as transfer line temperature may expand the metal but not the vespel ferrule.
For column conditioning, it is of course better to do it without connecting to the detector. However, the MS column e.g. DB-5MS is manufactured or designed for low bleeding operation and always claimed to be used directly without conditioning.

Yes. You are right. I really should follow the mannual, but my senior postdoc told me that it's fine to do just as he said. , so I trust the experience at that time.
Anyway, it is my fault.
I tried to tighten the nuts, but no change.
The O-ring, do you mean the one at the GC/MS interface? I didn't see it when I installed the column.
I could not perform the tuning at all for now. So frastrated.

wl,

For some reason I thought you were talking about LC-MS that is why your message didn't make any sense to me...

Sorry about that...

Can you try an air/water check (under diagnostics)?

Thanks a lot for all the replies. I really appreciate. So based on the above suggestion, I tightened the interface nuts and the nuts at the inlet, and restarted the pumping down. It has passed 30 min.......
Hope I will get better vacuum this time.

I capped off the column and got good vacuum, so the column and MSD part are good. Then I replaced the injetion septum and liner O-ring, reinstalled the column back to the injection port, and retightened all the fittings. After I've done all these, the vacuum went to 8~9*10(-5) torr again.

I have no idea where the leak might be. The only thing I can think is the gold-seal which was changed when I changed the column. I learn from the manual that every time the reducing nut is removed, the gold-seal has to be changed. Is this true? Also the washer? Will that cause the leak?

Any comments and advice are welcome. Thanks!

What is your column flow rate of the carrier gas? Please make sure that the flow rate is below the capacity of the vacuum pump that can sustain. For diffusion pump, never exceed 1.5mL/min (He) and 2mL/min for turbomoleuclar pump. Also for cap column, do not install column with i.d >0.32mm (without splitter).
Besides, check the GC instrument configuration for the cap column. Agilent 6890 actually "calculates" the column flow rate (either volumetric or linear flow rate) according to your input on column i.d. and column length, and GC then adjusts the column head pressure. That is to say, when you input 1mL/min., GC will calculate what column head pressure should be in order to give 1mL/min column flow rate. IF you give a wrong column i.d., column length, and the output pressure, the calculated flow rate will be totally incorrect.
Lastly, don't blame your postdoc any more. I don't think there is anything wrong related to column conditioning on this issue while GC column was connected to the MSD.

Thank you very much, chhubert.
(1) I checked spetrum scan in Manual tune, and saw about 10 ions other than 69 and 219. N2[28] is about 24% and O2 [32] is 10%. Since the ratio is not 4:1, it should not be air leak as you mentioned early. However, I am not sure if the contamination caused the low vacuum.
(2) About the column configuration and the flow rate. We have a turbomolecular pump and the DB-5MS (0.25mm * 30m * 0.25um). The old column was the same as this one, but I found its configuration was incorrectly set as 0.32mm * 30m * 0.25um when I tried to input the configuration for my new column. I corrected the configuration and kept the old flow rate (2.1L/min), ....., then I got the low vacuum and could not perform tuning. You are absolutely right. But I just don't understand why the system worked well with wrong configuration, while it failed with right configuration.
You are so insightful! Could you please give me some suggestion on what I should do now? Tons of thanks.

It is better to set the linear flow rate than the volume flow rate.

A leak at the inlet end of the column cannot affect the vacuum level, but it will cause nitrogen, oxygen and water to appear in your tuning.

After two years there is a good chance that the gas scrubber is exhausted - depending on use and how clean your cylinder gas is of course.

You need to get yourself a leak detector, they cost about the same as a capillary column. Restek sell a good one.

Peter

Yang,
Please also check the setting of the outlet pressure in the MS chemstation. As you connect the column to the MSD, you should select "VACUUM". The correct dimension of cap column and the outlet pressure are required for correct calculation of column flow rate (or in turn the column head pressure).
For the column that you are using, i.e. 0.25mm x 30m column, the optimium linear flow rate using Helium as carrier gas should be 30-40cm/s (or approximately 1mL/min). Therefore I suggest you to use 1mL/min instead of 2.1mL/min. When you set the column flow rate to 1mL/min, the ion gauge should read about 1 to 1.5x10-5 torr. If not, check the settings (column dimension, outlet pressure again) and make sure they are set correctly.
Notwithstanding this, I think your MSD system has air leak though the ratio of N2/O2 is not "exactly" 3:1, as MSD seldom detects both ions at the same time. I understand that small air leak is difficult to trace. However, you may take the advantage of MSD in checking where air leak is by using "REPEAT PROFILE" in the MANUAL TUNE. Please read the instruction laid down in the HARDWARE MANUAL and it'd tell you how to do it. Hope these help.