Agilent 5975T - first GC/MS purchase

[janoshik]

do you like the skin on your knuckles? avoid this instrument. its been replaced by the intuvo for good reason.

I will probably do so. I'll probably insist on a quote on a new machine.

Shimadzu quoted me well under 50k $ on a new system.

Thank you guys.

So far I'm very disappointed with local Agilent representatives, as the initial offer given during our talks had been 30% lower than the final one (without me adding anything) and even after complaining and shaving off warranty far under acceptable (and previously agreed!) 12 months to 3 months, it's still 20% higher than initial offer that I would take.

I was appalled by that. If I had been told a correct ( ie in 10-15% ballpark) estimate right away, I'd probably go for it, but this way I am not keen to do business.

I've decided to be cheeky and ask for a massive discount at Shimadzu for a brand new system, which would put it about 50% more expensive than several years old 5975T, while offering cheaper parts, maintenance, columns, 24 mo warranty and, it not being an integrated system, versatility.

Price difference on a refurb unit can depend on what they have in house at the moment. If it was very long after the initial quote, that unit could have been sold already and another that required more work to refurb could be what is being sold now.

According to rep, it's still the same - it was supposed to be as a backup unit at a different customers lab until 1. JAN 2020. That's why it surprised me even more.

[aldehyde]

Shimadzu is a good company and if you can get a good deal go for it, but be aware that there are reasons why their instruments are significantly cheaper than Agilent or Thermo.

[janoshik]

Shimadzu is a good company and if you can get a good deal go for it, but be aware that there are reasons why their instruments are significantly cheaper than Agilent or Thermo.

Well, over 5 years I have had exactly 0 service calls with Shimadzu, but I realize that a simple HPLC is far less prone to issues than, say GCMS.

I've heard bad things about their 2010 line GCMS, but only good stuff about 2020 line GCMS.

Seems like they have worked hard on fixing the rep.

[ThomasStegemann]

Might be even a good idea to bring Thermo into the equation. If you have 3 different offer for GCMS (and they all produce good machines) you have far more leverage over one vendor.

[benhutcherson]

It's worth getting a quote on Thermo, but I have to admit that after spending some time working on a relatively new ISQ in our department, I was not overly impressed, although that may be a lack of familiarity.

The one I worked on was pretty well stripped down in the sense that it lacked the no-vent feature and also an ion gauge. The one thing it did offer over a basic 5975 system was that it uses a turbo pump, although I've been very happy with my diffusion pump 5975. It was $44K in 2016, although bear in mind that we're talking academic pricing, which in my experience with Thermo is about 60% of retail.

Among my other complaints, I found the source very fiddly to remove, break down, and put back together. It doesn't have any wires that have to be manually disconnected, but on the other hand does need a special tool to remove the source(even on the one without the no-vent interlock). I managed to get it back together with one of the lenses rotated wrong, and we couldn't get it to tune after doing that. What made it even more frustrating was that accessing the manual tune window was difficult and even basic parameter adjustment defied my Agilent-minded brain.

Those are just my thoughts on it, but like I said it wasn't my favorite experience working on an MS.

[janoshik]

OK, will do!

Thank you for all the help and notes.

I assume Agilent is the golden standard, but I doubt I will be able to leverage them into conditions I'd consider acceptable

[ThomasStegemann]

Due to their high market share, they are somehow the standard that is right. But like i said the other vendors produce nice machines too. Look at their machines(ask for a demo) and see for yourself why their market share is growing constantly.
I cant imagine that agilent is keen on loosing you to the competition. But if they won't come down with the price it might be nice to have an alternative.

[janoshik]

Well, if anybody is interested, I managed to get a quote of $41000,- for basic 8860 with 5977B equipped with diffusion pump and $53000,- for Shimadzu QP-2020 NX with NIST and 150 position autosampler. Both with 24 month warranty.

Perks of living in pretty much 3rd world country I guess.

Shimadzu is on a completely different level spec wise, but frankly, I'm not doing any trace work nor high throughput analyses, so I am not sure I can justify spending that much for a higher spec system.

Still waiting on the reply from Thermo.

Thank you all for your input. It really helped me so far.

[benhutcherson]

That's a no brainer to me.

If you can, though, you might see if you can nudge the quote up on the Agilent to include a hi-vac gauge. Many of the bare-bones base model instruments don't have them, and I don't like not having one.

This comes back to the fact that many manufacturers often won't budge on the price, but sometimes you can get extras for the same price...

[janoshik]

That's a no brainer to me.

If you can, though, you might see if you can nudge the quote up on the Agilent to include a hi-vac gauge. Many of the bare-bones base model instruments don't have them, and I don't like not having one.

This comes back to the fact that many manufacturers often won't budge on the price, but sometimes you can get extras for the same price...

Do you mean Ion Gauge Controller?

If so, it's actually included - I apologize about my rookie question, but what's it good for? I mean, why is it necessary to know what is the vacuum level exactly?

[benhutcherson]

There are two components to an ion gauge-the gauge itself(which really is a vacuum tube) and the controller that makes sense of what is happening in the gauge. The 5975 uses a Granville-Phillips Micro Ion Gauge, which is a small box sitting at the back of the vac chamber via a KF-16 flange with a DB-9 type connector to the inside of the instrument. Agilent will hurt you for about $3K for the box(when mine went out, we were able to get a Granville-Phillips branded replacement for a few hundred dollars).

As for its utility-once the instrument is set up and working you can(should) be noting its normal operating pressure under a variety of conditions-including your "rest" conditions and at normal operating flow rates. Knowing if it has drifted from normal can be a huge help in diagnosing issues. Among other things, too, I generally you can see the solvent coming off the column by a spike in the pressure, which can help you set the solvent delay. Along those same lines, seeing things like pressure changes with flow rate or if there's a spike in pressure when you inject solvent can help spot issues like a blocked column.

So, put another way, it's just another valuable tool for me to monitor how well the instrument is running.

[janoshik]

There are two components to an ion gauge-the gauge itself(which really is a vacuum tube) and the controller that makes sense of what is happening in the gauge. The 5975 uses a Granville-Phillips Micro Ion Gauge, which is a small box sitting at the back of the vac chamber via a KF-16 flange with a DB-9 type connector to the inside of the instrument. Agilent will hurt you for about $3K for the box(when mine went out, we were able to get a Granville-Phillips branded replacement for a few hundred dollars).

As for its utility-once the instrument is set up and working you can(should) be noting its normal operating pressure under a variety of conditions-including your "rest" conditions and at normal operating flow rates. Knowing if it has drifted from normal can be a huge help in diagnosing issues. Among other things, too, I generally you can see the solvent coming off the column by a spike in the pressure, which can help you set the solvent delay. Along those same lines, seeing things like pressure changes with flow rate or if there's a spike in pressure when you inject solvent can help spot issues like a blocked column.

So, put another way, it's just another valuable tool for me to monitor how well the instrument is running.

Thank you!

[benhutcherson]

Here's a real-life example of how I've found a vac gauge useful:

Earlier today, a graduate student who uses a lot of GC-MS stopped me in the hallway and asked me an MS question. The crux of his question was why the base peak for his THF mass spectrum was 77(4 higher than the molecular weight). We talked it over as first of all it's pretty much inconceivable that anything would add 4 protons to THF at low temperatures in an inert atmosphere in GC, and I dismissed tuning/mass accuracy concerns since I'd just tuned it a few hours earlier and that's also very close to the 69 m/z cal peak.

Finally, I went down and looked at it, and the first thing I saw was that his data looked like noise to my eye even though the 77 m/z dominated-basically it was ~1000-2000 counts(randomly) with one vaguely discernible peak.

I went through troubleshooting, and the first thing I checked was the syringe(start with the simplest first) and it was working fine.

So, I think moved on to my next guess, which was a clogged column.

The first thing I saw with this was that the pressure was lower than I would have expected given the flow rate he was using. On this instrument, the gauge usually reads in the low 10^-5 torr range at that flow rate(diffusion pump instrument, .25mm column at .5mL/min). That tripped some alarm bells for me, so the next thing I did was raise the flow rate. In several steps, I got it up to 2mL/min and still didn't see a change on the hi-vac guage. At 2mL/min, it should have been reading close to 10^-4 torr.

Finally, I hand injected 1µL of DCM into it. This should have given a spike to 10^-3 torr or so within a minute of injection, but again I saw no change(although the inlet pressure did spike, as would be expected).

So, using the hi-vac gauge, I was able to diagnose a clogged column. Fortunately, that was a simple flx-I cut 6" off the injector in, and we were back in service. Still, though, the hi-vac gauge confirmed my suspicions and saved me a fair bit of diagnostic work.

[aldehyde]

That's a no brainer to me.

If you can, though, you might see if you can nudge the quote up on the Agilent to include a hi-vac gauge. Many of the bare-bones base model instruments don't have them, and I don't like not having one.

This comes back to the fact that many manufacturers often won't budge on the price, but sometimes you can get extras for the same price...

Do you mean Ion Gauge Controller?

If so, it's actually included - I apologize about my rookie question, but what's it good for? I mean, why is it necessary to know what is the vacuum level exactly?

You'll never know the "exact" vacuum level. The high vacuum gauges used on these types of MS are calibrated with N2, but GCMS uses Helium (I don't know why this is true, but it is.) This difference means it's not entirely accurate (pretty close)---but they are usually reproducible. If you find that your operating flow rate gives you a vacuum of 9E-6 you can expect to see something close to that day after day.

If you see you are not reaching your normal ultimate vacuum after maintenance, you usually have a leak, or perhaps the flow rate into the MS is higher than you normally run.

It is also useful because you can watch the ion gauge to identify the RT of the solvent peak.

If you are doing CI you can make sure that you're actually getting reagent gas delivered by adjusting the flow and watching the gauge, as well.

That price for the 8860-5977 sounds like a really good deal. The 8860 is a solid GC for sure.

[MSCHemist]

Running a GC/MS without a highvac guage is like driving without a speedometer. You can do it but you are missing vital information and will run into trouble.

I bought a used 6890+/5973N from Gentech for about $30k and it is still going strong about 6 years later with a few repairs (calibrant valve, rough pump, and usual consumables.

I also have a 14 year old 6890N-5975b. Same deal mostly vacuum system repairs filaments, a detector, 1 or 2 source parts and consumables. I took off the turbo and sent it to Pfieffer for a rebuild as the hi vac bearings were making noises at pump down and I wanted to get it serviced before it was EOL'd and parts were no longer available. It could probably see another 10 years of service.

the 73's and 75's have nearly identical EI sources and Restek and others sell those parts.