I bought a thing!: Adventures with a 20-year-old GCMS

Okay, I said I wasn’t going to make a thread until it got here but I’m just too damn excited! Since the wire officially cleared, I figured it was time to celebrate buying a Varian CP-3800 with a Saturn 2000 ITMS.

Big shout out to @cyclopath, @MagisterChemist, @Dr_Jebril and especially @Cassin for all the support they’ve given me. It’s nice to see other people excited about someone else’s project (especially when it’s mine!).

I bought a system complete with computer/MS Workstation for $4500 and immediately spent another $3k on columns and consumables, solvents, syringes, standards etc. Lol. I did buy an autosampler but the unit I bought doesn’t have a top cover which is necessary for mounting/locating the autosampler so now I have to find one of those. Honestly, there’s a couple other CP-3800s out on eBay for $800-$1000 and I’ll probably just buy one of those as a donor/parts machine. @cassin was kind enough to point out that it is apparently possible to run multiple 3800s off a single workstation so maybe I’ll keep buying up cheap machines and have multiples (should mitigate some of the “it’s way too old, it’ll break all the time” concerns).

I really hope I can share the process of getting it up and running, producing/validating results, and making this machine do some work for us. I settled on the system because they’re ubiquitous, inexpensive, and readily available (including donor machines, old stock parts, and even new manufactured parts). I’m hoping if I can make it work then other people will have a playbook to get them up and running.

Also worth mentioning that I have some specific reasons for wanting a mass spec (mostly high resolution OVI testing) and I understand most people would be more interested in FID but from my understanding, the FID is not a particularly complicated detector and the knowledge will still be applicable. Plus, if we can’t make the fancy sensor do what we need, maybe I’ll buy the candle sensor

Edit: pics, parts, and info to follow




I’m not sure what they have on there right now, but I see all kinds of lab equipment going at this site: Government Surplus Auctions - govdeals.com
It’s just another option for you to look at for “donor machines”!


I’m always on these auction sites looking for stuff! Part of my $3k included like 35 extra autosampler syringes for $45 lol, deals be everywhere!


They usually have all kinds of stuff there. The whole shipping thing is what sucks. You have show up to collect and ship on that auction site. Kind of sucks, but worth it. I saw a Shimadzu go for less than $350 last month. It was on a pallet that also included heated recirculating baths, and a couple other things. Crazy


There are certainly deals to be had. I can talk all day about the various markets of auction buying; I used to buy all our machine tools/tooling from auction buyers and I currently buy a ton of fittings/pumps/raw materials for our systems the same way and every sector has its own weird dynamics.

It seems like most of the auctioned analytical equipment goes to companies that bet the equipment is in working condition and have the know how to fix and “recertify” it if it’s not. Or just strip them for parts to rework the better systems. It also seems like they’re more interested in the auction units than the eBay ones, probably because most of the auctioned units were recently operating versus the eBay ones that tend to be “inherited” from some warehouse or liquidation. That last sentence doesn’t bode too well for the unit I bought lol


Oh ni-ice!!!


Super exciting. There are many great things you could do with this. One thing that would be nice is trying to clear up the “mystery soup” d8 confusion.


Sweet! Excited to see it come back to life.

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Yep! Mass spectra is certainly a nice thing to use to guess at what’s in the chili


Good luck with it and if you can post your journey here. I’m also interested in adding a GCMS to the stable but zero experience/background.


Hopefully I’ll be able to figure it out and share the process here. Right now I’m diligently waiting on my 7-10 day delivery lol


It’s here!!!

Very surprised at how complete it is although the recent vintage of the PC they sent with it has be a bit concerned. I was pleasantly surprised that this unit is optioned for chemical ionization which I guess is neat. Also stoked that it has the top cover to mount the autosampler to (which the ad said was missing).

I’m brutally busy right now so I probably won’t get to mess with it much for a few days but I’m super excited


Chemical ionization is nice for helping identify compounds not in the library. If you know how to break down mass spectra by hand.

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I know very little about it (pretty much just read about it in the manuals), but the concept makes sense to me. Nice to have an extra tool in the box at least


I’ve never used it, but there were some situations where i wished i could.

I am also super excited about this. It looks to be in great condition.

Did I tell you about cutting out the spectra by hand and weighing each piece to do a “back of the notebook” integration for compounds not in the library? There are other methods… but that worked great for me.

A presentation that talks about (almost anyway) the paper cutting method. They get specific about integrating the curves and looking for curve consistency. My method was specific to checking peak paper weights at specific retention times. Oh the times in the past. :smiley:

NIST has a giant library that is free online for different compounds ion patterns.

EPSRC UK has a library (which sometimes they give you access too…) but they will also take a sample you send them and tell you what it is with a dialed in spectra, if you want. Its always nice to have some academics lend weight to your arguments… at least I think so. muhahahaha! They also happen to be the group that puts together these great presentations for the “how” and “why” behind defining new spectra.

I cannot wait until you fire this up and share your progress! And I’m so glad it came with the parts it said it was going to be missing.


Yes you did and it is the coolest thing I’ve ever heard of! I’m going to get the workstation fired up and if I have even a little bit of trouble getting what I need out of it then the good 'ole dot matrix printer is going to be my next purchase.

I’m happy it even came with a column in it so I should be able to get it fired up, pumped down and checked for leaks and functionality while I’m waiting for all my other gear to arrive from restek. I was assuming I was going to need at least one thing that would need to be poached from another machine but I’m still holding off on buying a parts machine because so far it looks very complete.


The TIC (total ion count) method should eliminate all need for that paper. That is really a feature of not having integration software back in the day, not issues with the library.

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What I’ve been most worried about is getting the detector to communicate with the workstation as it seems a little new and I know getting the software to run and communicate on newer com ports is a little tricky. I figured if had to run TIC output to the printer directly I could at least start getting results

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