Chromatography Forum

A while ago, my organisation got rid of an Agilent 6890/5973N GC-MS and it went to the free e-waste disposal service (i.e. the back of my car). It's been sitting in my garage since and I'm wondering if it's worth getting it running for hobby use or even to do some small contract work? I also have the autosampler and a couple of capillary columns, but no plumbing.

Due to the COVID situation, the lab staff are the only ones on site. My colleagues joke around that if I could get the thing set up I'd be the only chemist in the department able to work from home

My background - I'm fairly new to GC-MS and LC-MS, having worked as a lab tech then analytical chemist for about a year and a half. Prior to this I finished a PhD in synthetic organic chemistry, with my only real chromatography experience (aside from flash columns!) being prep LC work purifying small peptides. Being a rather thrifty lab however, I often served as tech support for the instruments when we couldn't afford Agilent. We were also donated an old Micromass single quad, which I got running and kept going for a couple of years as a direct infusion instrument (until the electronics went bad not long ago).

So, anyone tried this at home? Is it as simple as getting the gas and go?

Back in March/April I had a stand-alone 5971 at home that I upgraded to a 5972. I got what I needed to done on it, but I didn't have a column installed of course. It was also a bear to get all the water out since I didn't have heater without the GC, but that shouldn't be a huge issue since you have both and also the 73 has heaters independent of the GC.

I've often thought of having one at home(I have a GCD here that's not hooked up and that I want to play with, and am debating about carting it into work or trying to get it going here) but there are two big issues I can think of even though neither is insurmountable.

One is that the GC will need a 20A outlet, something that not all homes have or at least have readily available. If you look at the plug on a 5890/6890/7890, you'll see that one blade is turned 90º to the other. If you look at most of the outlets, or at least many, in your lab, one hole(the right one IIRC) has a "cross" shape. This lets it take both conventional 15A plugs and the 20A kind. Very rarely have I seen a 20A outlet in a home, outside of course of the high voltage, high current ones for an oven and dryer. Most residential outlets are 15A. If you don't have one, don't be tempted to just drop a 20A outlet into the box-you really should have proper 20A service. In my experience, a GC oven heating up, especially at fast ramp rates, can easily pull that kind of current-I've tripped a breaker before even with two 5890s on the same(20A) circuit when both were hot and one kicked onto a ramp.

The second issue might be a bit easier, and that's having residential gas. Part of me is inclined to suggest hydrogen since it's a whole lot less expensive than helium. Another part of me, though, thinks of the fact that a garage or basement doesn't have anywhere near the kind of ventilation/air exhange as a lab. I never worry about even a leaky hydrogen line in the lab since it's so difficult to get to 4%, but it could be a different story in a tight home. Helium may well eat you alive on cost, especially if you are an individual rather than a business or organization. Can you transport a 300 sized cylinder or similar yourself? I know I can't lift one(or at least have never been brave enough to try). Airgas, Scott Gross, or whoever might not be so inclined to drive a truck into your driveway to drop it off they way they do at work. If you stick with helium, you might end up using "balloon grade" which realistically is PROBABLY fine but may be less than optimum.

Those are two big ones I can think of. Also, remember that if you're doing this out of pocket, that $100 you drop at work on a package of septa, $150 on a filament, $25 for ferrules, or $20/each on the good deactivated liners adds up quickly. Don't forget those $20/each Hamilton syringes, either. I know that's nothing for my work budget(or at least wasn't when I was at a big R1-I'm trying to get a 5973 sideboard now that's going to cost $1500-at U of L it would have been a poke my head in the chair's door and ask purchase, at the community college level it's a justification letter that goes to the president for approval). That adds up quickly if you're doing this out of pocket.

Back in March/April I had a stand-alone 5971 at home that I upgraded to a 5972.

That's interesting, I'd never really considered having a standalone MSD... what were you using it for if you don't mind me asking?

I've never encountered anything earlier than a 5973 in the field. Old equipment doesn't last long in our lab. Being in Australia, there's less surplus equipment floating around in general.

One is that the GC will need a 20A outlet, something that not all homes have or at least have readily available.

Domestic powerpoints here in Australia are all generally 10A. It wouldn't be terribly difficult to have an outlet wired into the house's 15A circuit, I may look into this. I didn't know that the 6890 needed 20A, I'll need to double check the points in the lab because I assumed they were all 15A...

The second issue might be a bit easier, and that's having residential gas. Part of me is inclined to suggest hydrogen since it's a whole lot less expensive than helium. Another part of me, though, thinks of the fact that a garage or basement doesn't have anywhere near the kind of ventilation/air exhange as a lab. I never worry about even a leaky hydrogen line in the lab since it's so difficult to get to 4%, but it could be a different story in a tight home. Helium may well eat you alive on cost, especially if you are an individual rather than a business or organization. Can you transport a 300 sized cylinder or similar yourself? I know I can't lift one(or at least have never been brave enough to try). Airgas, Scott Gross, or whoever might not be so inclined to drive a truck into your driveway to drop it off they way they do at work. If you stick with helium, you might end up using "balloon grade" which realistically is PROBABLY fine but may be less than optimum.

I could install a bracket for a G sized cylinder in my workshop. I was planning on using He, but I haven't worked out the total costs yet. H2 would certainly work as the cheaper option. I try to avoid it as much as I can (I used to do lots of high-pressure hydrogenations when I worked as a synthetic chemist and have a few scary stories). The workshop is very well ventilated being a converted carport rather than a properly sealed room. I run a small consultancy business on the side, so wondering if it would be easier to get gas in that regard. I may be able to install brackets for transporting cylinders in a trailer, so that'd make it easy to pick them up from the local depot.

Those are two big ones I can think of. Also, remember that if you're doing this out of pocket, that $100 you drop at work on a package of septa, $150 on a filament, $25 for ferrules, or $20/each on the good deactivated liners adds up quickly. Don't forget those $20/each Hamilton syringes, either. I know that's nothing for my work budget(or at least wasn't when I was at a big R1-I'm trying to get a 5973 sideboard now that's going to cost $1500-at U of L it would have been a poke my head in the chair's door and ask purchase, at the community college level it's a justification letter that goes to the president for approval). That adds up quickly if you're doing this out of pocket.

I haven't done a lot of GC maintenance (mostly just repairing HPLCs) but is it possible to rejuvenate liners? I anticipate running fairly clean samples, uncomplicated matrices, so I'm hoping that liners and other consumables could be stretched out as much as possible in terms of lifetime.

Something else I'm wondering is how GC-MSes take to power cycling. Not well, obviously, but I’m wondering if there’s some way that I could shut off the gas flow when not doing runs for a while, or at least reduce it to the barest minimum to conserve gas.

1. I wasn't actually "doing" anything with it, per se. Really what I did was take it home to do some major electronics upgrades(converted it electronically from a 5871 to 5972) and all I ever "analyzed" so to speak was PFTBA.

2. I forgot to look at where you were, and it was my mistake to assume US. At 220/240V, you SHOULD be fine with 10A service(which is roughly equivalent to 120V 20A), but double check the specs and make sure the plug fits.

3. If you can get gas, you're probably fine. I'm a big proponent of hydrogen in GC/GC-MS for a lot of reasons, even though it's not a universal solution. Remember that in GC applications, you're running RELATIVELY low pressures(probably not over ~100PSIG in your supply lines, and lower than that in the instrument) and also low flow rates. Hydrogen diffuses so quickly that at say a 5mL/min flow rate(which is really high for a capillary column) that in a decently ventilated space you won't get to 4%. Also, the HP/Agilent EPCs in the 5890 on up will shut down flow and other heated zones if they can't hit the pressure setpoint within a certain amount of time(3 minutes?) so you can avoid a bad leak or a broken column flooding your oven with hydrogen.

4. I have sonicated liners when they weren't super dirty, but for good quality analysis they should be replaced when dirty. In "emergency' situations I've even poked out the glass wool and put fresh in, but this isn't a great idea since even if you're using deactivated wool, you create active sites every time you break a fiber.

As to power cycling-one of the big issues is that, IME, MSs like to be under vacuum as often as possible. The longer they're open, the more crud the insulators and other such pick up(especially water), of course up to a point, while sitting under vacuum there's basically nothing to damage them. Another is that with a diffusion pump, it can be ~12 hours or better for one to stabilize after a pump down, and even turbos advise a minimum of 4 hours. You CAN turn off all the heated zones(in the GC and MS both) and otherwise leave it pumped down, but you have to be super careful with making sure you have let carrier gas flow for a while(to purge O2 and H20 as much as possible out of the vac manifold) but you're still going to need a little while for it to come to equilibrium and drive out any potential residual water. It should just soak up a lot less when under vac.

There are a few things I've done that help a fair bit with keeping idle gas useage down. One is setting up a rest method. For this, you set your flow low(with a 30mx .25mm column, you're going to be at ~1.1psi for a .5mL/min He flow at 50ºC, which is probably the bottom end of where you want to be to actually have the inlet at high enough pressure to keep air out), set your flow to splitless, and set septum purge off. Doing this, in my experience, will keep the gas useage to maybe 100psig off the tank every couple of weeks, which is decently low.

One that I did at my last institute was fit a carrier/nitrogen changeover valve on the line supplying all the GC-MSs(the room was plumbed to supply 2x GC-MSs, 4x SRI GCs w/TCD and FID in series, and a seldom used 5890 with an FID and dead NPD). My GC-MSs in that room always ran helium. They were also used sporadically-sometimes they'd be run a couple of hours a day every day, sometimes they'd run nearly continuously for a couple of weeks, and sometimes they'd be idle for a few weeks. We had two, BTW(one of which I "resurrected" from a corner of another lab), mostly because more than one person would need daily access to them at the same time . In any case, though, at the end of the day or the end of a period of use, I'd use a valve to switch the carrier flow over to N2. I was paying ~$200 for He(5 9s), ~$50 for H2, and ~$17 for N2, also UHP 5 9s. At those prices, using N2 in the resting times saved a lot of money. If using H2, it also has the benefit of flowing an inert gas when not actively in use, which makes things somewhat safer. It took about a half hour to stabilize back out with He after running N2. I got the idea from the fact that 7890 and 8890 have an add-on to do this automatically.

One last thing-do you have software to run this?

For the power, in US it is 120V 20A, if you have 240V in Australia then you may get away with 10A, just have to check the spec sheet for the 6890, which should be available at the Agilent website.

I clean liners all the time myself. Some I can just sonicate or soak to remove any residue. What I do is a sequence of water/citranox solution, the DI water, then Methanol, then Methylene Chloride. Put the beaker in the GC oven at 50C for a half hour and they are ready to go. If they have char or oily residues I can put them in a muffle furnace at 450C for a few hours, then just solvent wash and they are usually good go to. If you are doing analysis of really fragile pesticides then you may need to hit them with some CylonCT to silanize them and remove active sites, but for something like hydrocarbons, fats, waxes, and PCBs you really don't have to worry about having them completely deactivated.

For gasses, Helium is best for MS, and a standard sized cylinder will usually last for several months running a single instrument, I think I have even gotten 6 months out of a cylinder on a single instrument so that isn't too terrible on expenses. Hydrogen will be less expensive and if you can find a good hydrogen generator more cost efficient and less prone to problems with leaks since most will sense a leak and shutdown. Just have to supply them with DI water. If you get the more expensive hydrogen generator with the palladium membrane you don't have to worry about moisture, if you get the less expensive one with the desiccant then you will need to use inline moisture traps to keep the moisture out of the system.

If you will hook up the roughing pump to as wall outlet instead of using the electronics on the MS, you can keep it under vacuum without having the GC and MS running constantly, just need to cap off the inlet to the MS, then you can quickly insert the column back in before powering up, and the system will come up within a day and be stable. Also you can just set the flow on the GC to about 0.5ml/min, and a 5ml/min split flow and leave everything warm and under vacuum as a standby, which is what I would prefer. At those settings a tank of gas could last you a year.

Thanks for the suggestions everyone. I've now set up the unit on a table in my garage. When I took it home, I didn't have time to take stock of what was missing - it will need a new ion source assembly, syringe for the injector, possibly a remote cable for the autosampler and I'll need to get some fittings so that I can install a KF flange on one of the roughing pumps I have lying around.

I collected some used, to-be-discarded liners from the lab and will hand them off to some of my contacts at my old (synthetic) lab to get cleaned (if they have a bit of spare time).

Next, and biggest hurdle logistically, will be the gas. I like the idea of having a valve in the line to switch between N2 and He. Given that the GCMS isn't installed in my own workshop, I don't want to introduce the potential liabilities of having H2 at home.

If I end up making any more progress with this project, I'll post up some updates here. Otherwise, it may just become a source of parts whenever someone calls in a favour to repair their equipment...

3. If you can get gas, you're probably fine. I'm a big proponent of hydrogen in GC/GC-MS for a lot of reasons, even though it's not a universal solution. Remember that in GC applications, you're running RELATIVELY low pressures(probably not over ~100PSIG in your supply lines, and lower than that in the instrument) and also low flow rates. Hydrogen diffuses so quickly that at say a 5mL/min flow rate(which is really high for a capillary column) that in a decently ventilated space you won't get to 4%. Also, the HP/Agilent EPCs in the 5890 on up will shut down flow and other heated zones if they can't hit the pressure setpoint within a certain amount of time(3 minutes?) so you can avoid a bad leak or a broken column flooding your oven with hydrogen.

I'd absolutely love to use hydrogen in the lab, instead of helium, but I'm getting 500 ml/min flows with the splits I'm running and it's hard being comfortable with that in a tiny lab space we have for our GCMS

I'd absolutely love to use hydrogen in the lab, instead of helium, but I'm getting 500 ml/min flows with the splits I'm running and it's hard being comfortable with that in a tiny lab space we have for our GCMS

Have a "gas saver" function on your GC ?

I'd absolutely love to use hydrogen in the lab, instead of helium, but I'm getting 500 ml/min flows with the splits I'm running and it's hard being comfortable with that in a tiny lab space we have for our GCMS

Have a "gas saver" function on your GC ?

yes I do and I use it as much as possible, but anyway, a while before the injection, during injection and a while afterwards you need. so in the end you have at least 3-4 minutes of very high flow out of split vent

also, I've had an employee forget to turn on the eco mode and we had 500 ml/min flow turned on the entire night, so I'm not keen on switching to hydrogen

I'd absolutely love to use hydrogen in the lab, instead of helium, but I'm getting 500 ml/min flows with the splits I'm running and it's hard being comfortable with that in a tiny lab space we have for our GCMS

Have a "gas saver" function on your GC ?

yes I do and I use it as much as possible, but anyway, a while before the injection, during injection and a while afterwards you need. so in the end you have at least 3-4 minutes of very high flow out of split vent

also, I've had an employee forget to turn on the eco mode and we had 500 ml/min flow turned on the entire night, so I'm not keen on switching to hydrogen

Run a line from the split vent through a hole in the wall to the outside air, it is how we used to do it in our old building. Or into a fume hood if you have one of those near. On something like a 5890GC the split vent has a 1/8" swagelok fitting so you can either plumb copper tubing to it or just use some 1/4" tygon slipped over the fitting and run outside.

Another option of you like would be to plumb the split vent into a bunsen burner and light it and just burn off the excess hydrogen.

Have a "gas saver" function on your GC ?

yes I do and I use it as much as possible, but anyway, a while before the injection, during injection and a while afterwards you need. so in the end you have at least 3-4 minutes of very high flow out of split vent

also, I've had an employee forget to turn on the eco mode and we had 500 ml/min flow turned on the entire night, so I'm not keen on switching to hydrogen

Run a line from the split vent through a hole in the wall to the outside air, it is how we used to do it in our old building. Or into a fume hood if you have one of those near. On something like a 5890GC the split vent has a 1/8" swagelok fitting so you can either plumb copper tubing to it or just use some 1/4" tygon slipped over the fitting and run outside.

Another option of you like would be to plumb the split vent into a bunsen burner and light it and just burn off the excess hydrogen.

Good ideas, thank you! After Holidays I'll check on the possibility of doing that.

2 minute GCMS screening methods, here I come.

Hi mate,

Where abouts are you located? I'm in Sydney. Would be interested to chat to you about your setup as I have contemplated doing something similar.

Thanks!

Hi mate,

Where abouts are you located? I'm in Sydney. Would be interested to chat to you about your setup as I have contemplated doing something similar.

Thanks!

I'm in Melbourne. I have the system (6890/5973N) assembled but not functional - I still need an EI source and a bottle of helium. Haven't tested any of the electronics yet.

You can email me at wss.ion.trap@gmail.com

So, three years on and I have this semi-set up in my shed at my current residence. No helium yet, no vacuum pump and no ion source.

Does anyone know what the latest version of MassHunter is that will work with a 6890N/5973N? This instrument was probably running Chemstation E.02.02 before it was decommissioned but I'd prefer to use MH if possible. I do have E.02.02 and licence if I can't get MH.

So, three years on and I have this semi-set up in my shed at my current residence. No helium yet, no vacuum pump and no ion source.

Does anyone know what the latest version of MassHunter is that will work with a 6890N/5973N? This instrument was probably running Chemstation E.02.02 before it was decommissioned but I'd prefer to use MH if possible. I do have E.02.02 and licence if I can't get MH.

Pretty sure the lowest model officially supported by MassHunter is the 5975C with 7890, but I have read there are hacks to make it work with 5973s but not sure of the 6890.

E.02.02 works with W11, but make sure you have any antivirus disabled when installing as come catch a couple files that are needed to make it work. It can be a little buggy, and normally you will need to disable any network card not connected to the instrument (such as using dual cards for house network and instrument) when starting the software, they can be enabled after startup.

I have MH 7 and MH 10, I like MH7 better as the tuning window is more like the MSDChemstation and the newer version is a little weird.