Shutting Down GC-MS System

Discussions about GC-MS, LC-MS, LC-FTIR, and other "coupled" analytical techniques.

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Hello Everyone,

I am new to the forum and full disclosure not an expert at GC-MS systems. However, I am a chemistry professor at a small liberal-arts school which kind of makes me a jack of all trades and puts me in charge of our instrumentation (I have the most experience of the faculty here). Anyways, we recently purchased and installed a refurbished Agilent 6890-5973 GC-MS system using He gas as our carrier. Currently, this instrument will only be used for teaching purposes, meaning it will only be used a couple of times of year in our Instrumental Analysis course and not for very sensitive quantitative work. With money always tight, I was wondering if it would be okay to shut the system down while it is not being used to conserve He gas. I know it is preferred to keep the system on and pumped down and gas flowing, but we are working to save as much as money as possible, and since the instrument will sit idle for several months, it seems somewhat wasteful to keep it running.

So first, is it possible to leave the MS system under vacuum without the carrier gas on? I would guess this means turning the temperature down or off on the filament, which is fine if it is possible. I also know we would need to set the GC oven temperature to ambient while it is shutdown. So any advice I could receive from the experts here is GREATLY appreciated! We want to teach our students the importance of GC-MS, but also do so in an economic fashion!

Thanks again for any help!
This may be unorthodox, but I'd consider it fine to leave the MS pumped down and the quadrupoles warm with the He off.

The filament and ion optics are only "on" during a run-they don't get turned on until after you've started the run and the programmed solvent delay has passed, and then get shut off at the end of the run. The same is true of the electron multiplier.

I WOULD leave the quad heater on all the time.

I'd go in and turn off the oven, inlet heater, and transfer line. Once they're at ambient, you shouldn't hurt things too much by shutting off the carrier. Just turn the helium on and get it flowing at ~.5mL/min or better for several minutes before heating things back up-this should be sure you've purged all of the oxygen out of the column before heating.

I went to a small liberal arts college, and we had a 5890/5971 that didn't even get this treatment. The inlets stayed at 250º all the time(this system had both an FID and the MS), and both the FID and transfer line stayed at temperature. We would just shut off gases at the tank when done with it, and would set the oven to 40º(not oven off). The system was still on its original HP-branded columns and working great when I graduated in 2010(when the system would have been closing in on 20 years old). It wouldn't surprise me if they're still using the same columns.

With that said, my 7820/5975 runs at .5mL/min under the "rest" method, and with on average 50-75 hours of use a month I generally lose 300 psi out of the cylinder a month. That also includes intermittent use with 4 packed column GCs that use a TON of helium when on(~100 psi a day) plus a 5890 that I run at a fairly low flow rate all the time. On months where the GC-MS has had minimal use and the other GCs have been shut off, I see a loss of more like ~100 psi a month. With your use case, I'd guess you could get 18 months or better out of a cylinder even with it on all the time.

Regardless of whether the carrier is running, I'd suggest leaving the MS under vacuum all the time. When I've brought systems that have been open and vented for extended periods of time(weeks to years) it usually takes a week or better for them to stabilize and start giving good results. Repeated vent and pump down cycles are not that good for the MS, plus can leave you chasing your tail trying to get them going.
My experience is that things work better when they run but I do understand your dilemma. Most of us are probably not in your situation. My systems need to be up and ready all of the time.

You can turn it off completely when not in use. Just make sure that you follow the instructions for venting the system (Chemstation dictates how this should go so it shouldn't be a problem). Seal it up tight by putting a blank ferrule (no hole) and nut over the inlet to the MS. If you choose this route, you'll need to start bringing it back up a few days in advance to make sure that you get all of the air/water out of the system. Just like with computer systems, most castrophic failures occur during startup. Is failure and subsequent replacement of a MS detector cheaper than $100 (pulling this number out of a hat, I don't know how much we pay for helium) a month for helium?

You don't want to leave vacuum on with no flow. You'll pull in air and if it's hot and you're pulling in air, many problems will result. If you leave the vacuum system up, you'll need to seal off the inlet to the MS with a blank ferrule. That means venting to remove the column then pumping it down again. This can be a good troubleshooting check for finding leaks that are related to the column. I don't know if I see an advantage to this approach. Perhaps my esteemed colleagues will have other compelling reasons to do this.

If it were me, I'd probably shut it down completely if it'll only be used twice a year and I really couldn't afford the helium. You could also turn the head pressure on your column down - just make sure to keep positive pressure on the column and thus on the MS.

Can't find more uses for it to justify keeping it running all the time? Any research going on in your department that might need some volatiles testing? Spread the maintenance costs around a little?
I have a 5973 that seldom gets used, is switched to nitrogen when not in use. Just remember to switch back to helium the day before. Agilent sells a version of this on new GCs and has a flush feature so it doesn't take hours to chase out the last of the nitrogen.
The nitrogen comes from a 2000 liter Dewar of liquid so your application may vary.
Steve Reimer wrote:
I have a 5973 that seldom gets used, is switched to nitrogen when not in use. Just remember to switch back to helium the day before. Agilent sells a version of this on new GCs and has a flush feature so it doesn't take hours to chase out the last of the nitrogen.
The nitrogen comes from a 2000 liter Dewar of liquid so your application may vary.
I also do this. I have a 5890/5971 back up system and I keep it hot under vacuum with UHP nitrogen from a dewar in my lab. As Steve says, I switch back to helium a day before I use it.

Definitely do NOT try to keep vacuum with either an oil diffusion pump or a turbo pump without flow. I suppose it might be OK to shut down the system but keep it partial vacuum on it with a rough pump. When I rebuild a source, I take out the source for cleaning and put the rest of it back in and let the rough pump keep a partial vacuum on it under the theory that there will be less chance to absorb water, etc. I suppose that could be done indefiniately. But I wonder about back flow over extended time from the rough pump.
Hello Everyone,

Thanks for your quick and informative replies! I really do appreciate it. From reading through the replies so far, I am wondering if just dropping the flow to a low rate would be the better option. Our method we are currently using runs at 1.2 mL/min and when the service engineer left he mentioned keeping that flow rate on the system. I thought this was the recommended flow rate to keep things from overheating and from having back diffusion issues with the pumps. However, I do not think he fully appreciated how little we would be using the system at first. What is the lowest flow we could run at and not have to worry about these problems? We have a Rtx-5MS column, 30 m, 0.25 mm ID, and 0.5 um df.

Again, thanks for your help!
I'd say you could drop your head pressure to 1 psig and be ok. Try that and see if it works. If you get an alarm for too low of a pressure in the inlet, raise the pressure until it quits. I have had alarms like that before when I dropped my GCMS into a "STANDBY" method like that.
With essentially the same stationary phase, column length, and ID my rest method is .5mL/min. I can't access my system at the moment(power failure) but I'd guess offhand that's a head pressure of ~5 psi with that column(11psi gives ~1mL/min)

Like I said, if I'm not pulling anything else off the cylinder this is good for about 100psi a month.
Thanks again for your quick responses! Last question, I promise. I dropped the flow rate down to 0.5 mL/min. My final question is, is the inlet gas flow (splitless) always running? We have the gas saver on at 15mL/min, the lowest it can go, but is that flow always on, or only when the instrument is ready for a sample injection?

Thanks again everyone!
PUI Prof wrote:
Thanks again for your quick responses! Last question, I promise. I dropped the flow rate down to 0.5 mL/min. My final question is, is the inlet gas flow (splitless) always running? We have the gas saver on at 15mL/min, the lowest it can go, but is that flow always on, or only when the instrument is ready for a sample injection?

Thanks again everyone!


If you are running 0.5ml/min on the column turn off the gas saver and set the split flow to 10:1 or 20:1 so that the total flow is only 5-10ml/minute. At that flow rate a cylinder of He will last at least 6 months. You could also switch to UHP Nitrogen for the standby, easy to do since they have the same cylinder fittings.
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