Running H2 on 5890/5971 GC-MS OK?

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

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Has anyone got experience running Hydrogen on the 5971 GC-MS? Helium is getting so expensive. I can't find anything in the 5890 series II GC manual nor the 5971 manual that says I can't. So, it should be OK as long as I remain vigilant for leaks.

I just installed a 3-way valve on my 6890N/5973inert (standard turbo) and switching from 1 mL/min He to 1 mL/min H2 raised my apparent vacuum from ~3.3E-5 Torr to 1.0E-4 Torr. So since its calibrated for N2 (factor=1); He factor is 0.15 and H2 factor is 0.46 so increasing the factor should push me up pretty close to 1.0E-4 Torr. Am I thinking about that correctly?

I'm going to do the 3-way valve on the 5890/5971 system next if its safe.
I've not personally done it, but don't see why it wouldn't work-it's not like Varian ion traps where they splash warnings all over the place about using H2.

Also, it's worth mentioning that the EPC on my 5890/5971 has an H2 option, as does the electronic flow meter on my 5890 FID/NPD. The EPC also goes nuts and shuts everything off(requiring power cycling to clear) if it can't reach the set point pressure-the manual claims this as a safeguard against hydrogen leaks(it makes a rather angry beep the likes of which I've never heard the 5890 make).

Diffusion pumps work well with H2, so you're good to go in that respect. Your pressure also sounds within reason. I'm use to somewhat lower pressures on He than you mention, but I also run an overspecced rough pump(Varian DS102 rather than the Edwards E2M2).

You PROBABLY know this, but just in case-remember that the viscosity of hydrogen is somewhat different from that of hydrogen. If you're basing your flow rate on something like HP Flow Calc, just be sure you've selected H2 as your gas and adjusted the head pressure accordingly. Needless to say, with the EPC, you need to also specify H2(I think you'll have to go through and change this on every method).

Agilent does sell a modified draw out plate meant for H2 use in the 5973/5975 that has a much larger hole. It might be worth sticking one in a 5971. https://www.agilent.com/store/en_US/Pro ... 2589-20045
I ran hydrogen on a 5971 about 20 years ago. It worked well except that I was doing EPA Volatiles and the BFB tune check wouldn't pass.

The vacuum will look higher on the gauge but that is due to the calibration and different response for H2 versus He as stated above. The only Agilent MS I have seen with a problem with Hydrogen are certain 5975 models that have the wrong type of magnets. I think the ones without a serial number on them are not compatible with Hydrogen, which just happen to be what we have on the two 5975s we have, but the proper magnets can be ordered and swapped out, all the rest are compatible.
The past is there to guide us into the future, not to dwell in.
I know I have the right magnet in my 5973 and I have the 6mm internal diameter draw out plate. It had not occurred to me to try that draw out plate on the 5971. Can I assume the magnet on the 5971 is up to the task?

I put the system on hydrogen over the weekend and a blank run has 20K counts of background that resembles that of oils but only out to mass 128 or so. However, peak shapes are excellent (no drag) and in addition, those masses are very low in scan. Cannot even see it with EV below 1100V. Tune on my 5973 at the moment is running with EV at 1400. Setting EV to 800V as in this link... https://grupobiomaster.com/wp-content/uploads/2016/11/Conversion-of-Agilent-EI-GCMSD-systems-to-H2-carrier-gas.pdf
results in the scanning being automatically stopped because there are no peaks.

I'm guessing that the background is not in the source but maybe the gas, the column, the EPC, or the inlet plumbing. I have one of those big hydrogen cleaning filters from RESTEK just after the cylinder. Its seen over a dozen cylinders of UHP Hydrogen so I think that is probably the problem.
When switching to hydrogen you almost always see the "hydrocarbon" background in the spectrum. The older and longer the system has run on helium the worse it will be.

When I tried hydrogen on my 5973 in the volatiles lab I had it on hydrogen for a month and there was still a little of that noise, though it had finally dropped to a level that didn't interfere with anything. When I switched that system back to helium it had the cleanest background I have ever seen. I was tuning with 69 at about 500k counts and getting maybe 10 peaks in the spectrum with the valve closed. The hydrogen does a good job of cleaning the entire system.

I have a manual switching valve installed on my 7000 and will set it to hydrogen for a weekend to help clean it up, works great.
The past is there to guide us into the future, not to dwell in.
Its reactive with compounds too. My dibromofluoromethane surrogate looses half its area under hydrogen versus helium carrier. I normally run with inlets and xfer line at 200C. Do you think dropping the inlet to 150C would be a good idea or just cause problems with heavy compound recoveries?
I have run volatiles with the transfer line at 150c most of the time, and inlet at 150-180c without problems, even when including naphthalene and trichlorobenzenes.

Also check to make sure it is just losing sensitivity or if it is adding 1 to a mass due to CI happening with the hydrogen. It happens with BFB where the 95/96 ratio is messed up because of that.
The past is there to guide us into the future, not to dwell in.
LALman wrote:
I know I have the right magnet in my 5973 and I have the 6mm internal diameter draw out plate. It had not occurred to me to try that draw out plate on the 5971. Can I assume the magnet on the 5971 is up to the task?

I put the system on hydrogen over the weekend and a blank run has 20K counts of background that resembles that of oils but only out to mass 128 or so. However, peak shapes are excellent (no drag) and in addition, those masses are very low in scan. Cannot even see it with EV below 1100V. Tune on my 5973 at the moment is running with EV at 1400. Setting EV to 800V as in this link... https://grupobiomaster.com/wp-content/uploads/2016/11/Conversion-of-Agilent-EI-GCMSD-systems-to-H2-carrier-gas.pdf
results in the scanning being automatically stopped because there are no peaks.

I'm guessing that the background is not in the source but maybe the gas, the column, the EPC, or the inlet plumbing. I have one of those big hydrogen cleaning filters from RESTEK just after the cylinder. Its seen over a dozen cylinders of UHP Hydrogen so I think that is probably the problem.



I run my 5890/5972s on H2. It's hard on the factory quads, but if you switch to metals quads it works just fine. Long ago we drilled out all of our draw-outs to 6 mm; you get a huge increase in signal on the '72s. I literally did it with a drill bit and a Dremel; not the most elegant work I've ever done but functional.

I like the vacuum; since my '72s are DIF stacks it's quite efficient, better than what we got with He. No idea what would happen on a turbo system; I would guess that you might get less turbo life with H2 impinging on the blades (reactive) and probably degraded vacuum since turbos don't like light gases.

We have had to up our maintenance on the rough pumps to oil changes every 6 months rather than every year. I saw the "hydrocarbons from hell" problem for about 6 months after we switched over; now it's just the "samples from hell" but nothing I can do about that !! :lol:

We generate our own H2, so it's really pure. Haven't tried it off of a bottle; not sure what you'd get for purity. We did switch the P&T over to N2; I just have this pit-of-the-stomach thing about flowing hydrogen over hot catalytic surfaces.
Mark Krause
Laboratory Director
Krause Analytical
Austin, TX USA
mckrause wrote:
Long ago we drilled out all of our draw-outs to 6 mm; you get a huge increase in signal on the '72s. I literally did it with a drill bit and a Dremel; not the most elegant work I've ever done but functional.


Your comment has me thinking about the draw-out hole diameter. I'm wondering if it's worthwhile to do even when running He.

Part of me thinks that since Agilent makes/sells the 6mm plate, they would use it in everything if there was an advantage(particularly singe I'd venture to guess that He is still most common). It DOES certainly make sense, though, that a larger one would increase the number of ions making their way into the quads. I'd be afraid of increased noise with it too, though.

I'll keep my eyes open for a dead/junk 71/72 as I hate to modify the one in it now. If there is an advantage, I'd do it on both my 71 and 75.
benhutcherson wrote:
mckrause wrote:
Long ago we drilled out all of our draw-outs to 6 mm; you get a huge increase in signal on the '72s. I literally did it with a drill bit and a Dremel; not the most elegant work I've ever done but functional.


Your comment has me thinking about the draw-out hole diameter. I'm wondering if it's worthwhile to do even when running He.

Part of me thinks that since Agilent makes/sells the 6mm plate, they would use it in everything if there was an advantage(particularly singe I'd venture to guess that He is still most common). It DOES certainly make sense, though, that a larger one would increase the number of ions making their way into the quads. I'd be afraid of increased noise with it too, though.

I'll keep my eyes open for a dead/junk 71/72 as I hate to modify the one in it now. If there is an advantage, I'd do it on both my 71 and 75.


Don't the drawout plates from the 5973's also fit the 71/72 source? If so then you can order a larger one.

On our 7000 I am using a 9mm drawout which they sell with their low level PAH setup, and it works great for the full list of 8270 analytes.
The past is there to guide us into the future, not to dwell in.
James_Ball wrote:
Don't the drawout plates from the 5973's also fit the 71/72 source? If so then you can order a larger one.

On our 7000 I am using a 9mm drawout which they sell with their low level PAH setup, and it works great for the full list of 8270 analytes.


I can't see why they wouldn't fit. The ion optics themselves are the same AFAIK 71-77. I know at least that when I ordered a lens insulator a few months back(after checking with Brenda) I ordered the 73/75 one and it fit perfectly aside from being that annoying 1-piece design that I detest.

Since the draw-out plate sits in the same position in the source body on the 71/72 as the 73 and I know the rest is the same diameter, I don't see why the larger diameter one for the later instruments wouldn't fit.

It would be about $130 delivered to use after discount to buy...if I could find a dead one for free or not much more to scavenge parts like that from and modify one, I'd try that route as it seems a simple modification.
benhutcherson wrote:
James_Ball wrote:
Don't the drawout plates from the 5973's also fit the 71/72 source? If so then you can order a larger one.

On our 7000 I am using a 9mm drawout which they sell with their low level PAH setup, and it works great for the full list of 8270 analytes.


I can't see why they wouldn't fit. The ion optics themselves are the same AFAIK 71-77. I know at least that when I ordered a lens insulator a few months back(after checking with Brenda) I ordered the 73/75 one and it fit perfectly aside from being that annoying 1-piece design that I detest.

Since the draw-out plate sits in the same position in the source body on the 71/72 as the 73 and I know the rest is the same diameter, I don't see why the larger diameter one for the later instruments wouldn't fit.

It would be about $130 delivered to use after discount to buy...if I could find a dead one for free or not much more to scavenge parts like that from and modify one, I'd try that route as it seems a simple modification.


Restek did the same thing with modifying the drawout plate diameter in a test to see the difference, I think at 9mm they had to modify the one for the 73/75, the 7000 uses the extractor lens where the drawout plate and the ring with the slots are one piece, but Agilent makes it in three diameters up to 9mm.

https://blog.restek.com/?p=13930
The past is there to guide us into the future, not to dwell in.
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