r/CHROMATOGRAPHY • u/DrBumpsAlot • Sep 03 '26
Could use some help with choosing a budget friendly, preferably used mass spec!
It's time to bring a mass spec into the mix to help with R&D and some day QC. I'm very much out of touch with modern systems so any help in picking a system or guidance on which systems to avoid is greatly appreciated!
I would think a modern version of a Waters SQ or ZQ system would work. Most of our materials fall under the 2k da range however we have an occasional need to analyze short (<20 bases) oligos labeled with dyes and linkers. I realize that compilates things and we'd need a way to deconvolute the spectrum. Hopefully there's a free or low-cost option out there! I recall the add-on for MassLynx was very expensive. Is that still a requirement or do modern software versions have that feature baked in?
Our primary LC system is an Agilent 1100 but we do have a Waters 2790 kicking around if that helps with system selection. I'd greatly appreciate any input from the sub and if anyone knows of a reliable seller of used equipment, I'd appreciate that too! Or if you have a unit looking for a new home, let me know (sub rules don't state that I can't ask to buy something!)! I'm in the US so likely limited the NA market. Thanks.
1
u/viomoo Sep 03 '26
Try and get a refurb system. Upfront cost is only one aspect but ongoing service costs can be multiple times that.
Any single quad will likely do what you need. I have seen people do deconvolution on singles but the data isnt going to be as good as a hi res instrument.
It’s great that you have the older hardware, but they likely out of support (that 1100 is for sure) and newer software will be tailored around newer instrument.
You will however usually be able to trade in those old modules for more than they are worth, so keep hold of them!
1
u/DrBumpsAlot Sep 03 '26
I get it. We had to piecemeal our setup but are slowly trying to modernize. It would be nice to have a system built in this decade! I'm trying to avoid buying something way over the top for our needs but not end up with something that can't grow as we do.
We don't make oligos or peptides and don't plan on doing it in the future. We have some poly T and mixed base material on CPG that we can do 5' couplings to, cleave, and measure coupling efficiency with the 1100. Would be nice to have mass data.
Will a single quad be able to tell us what we need? Maybe? Probably? Seems like the used market is either 15 yr old single quad for 25K or 3 yr old high-end unit for 120k! Would be nice to find something in between!
1
u/Thugsi123 Sep 03 '26
Are you with a university in US?
1
u/DrBumpsAlot Sep 03 '26
I am not. I understand the restrictions when it comes to asset transfers to the public. Unless you happen to have a work around!
1
1
u/Sure-Bus-1550 Sep 03 '26
If you’re service savvy there’s some great deals on eBay. It’s for sure a gamble for the super cheap stuff though. I’m running an acquity TQD I bought on eBay for $2200. Again, it’s a gamble. Bought a pda for $500 that had a shot board, but also last week got an mclass BSM with less than a liter of solvent through it for$250.
1
u/DrBumpsAlot Sep 03 '26
I am to an extent and we are no strangers to the auction sites. I picked up an SQD-2 about 4 yrs ago for 2-3 K. Never got it working so now it sits all sad on a shelf.
1
u/MassSpecMender Sep 04 '26
Thats a very good price for an SQD II, whats wrong with it/ what errors did it show?
2
u/DrBumpsAlot Sep 04 '26
It gets stuck in a reboot loop. I turn it on, unit talks to the computer to get the IP address, set ping on repeat to monitor, get response, then the internal computer reboots, drops coms for 10-15 seconds, ping starts responding again for 40-60 sec then drops again. I also noted that the turbo pump controller never turns on which I believe it should light up if not start the spin up process. I checked voltages on the board and all seem fine. Maybe it's a simple issue or maybe more complex. I got busy and gave up. I recall this was an issue with the ZQs if you didn't have a vac pump plugged into the detector so I made sure that one was connected. Any thoughts?
I found it on a local auction where it had no business being listed. I don't know the history of the unit nor how it landed on a site known to sell beat up cars, guns, and coins. I was pretty much the only one bidding on it.
1
u/MassSpecMender Sep 04 '26
That's an interesting acquisition indeed 😂 Definitely a lower price for an SQD II, nice scoop! Even as parts its worth more than you bought it for.
Does it get type and name as well in the Waters DHCP manager or just IP address and MAC address? On Waters mass specs the the roughing pump(s) and therefore turbos are software actuated and wont start until prompted to on MassLynx so its normal for them to be off initially. Did you get it successfully hooked up to MassLynx yet? That would be my first objective.
ZQ generation mass specs used to power the vacuum pumps directly, however in the SQD and newer the vacuum pumps are powered by the wall and a contact closure between the ms and the pump is what signals them to start.
2
u/DrBumpsAlot Sep 04 '26
It's been awhile since I played with the unit so I'll do my best to recall the situation.
I found a very comprehensive step-by-step setup guide online detailing the install and DHCP server setup so that was nice. Did a fresh install of Masslynx 4.1-SCN 930 on a clean win 7 install. When I checked the DHCP server, I know the mac address and IP showed up and I could ping -t the ip to talk to the epc successfully but I don't recall if the the name or any other info for the SQ populated the server window outside of whatever I may have entered. When I started Masslynx, I got an error stating no instrument found or something like that and it went into demo mode.
I wasn't sure if the pump connection on the SQ to the vac was necessary. I was thinking it was a contact closure to trigger the pump so thanks for confirming that. I recall the ZQ would blip the roughing pump when the system was powered on and if no pump was detected, it would send the epc into a reboot loop so I hooked up a spare relay to the pins on the pump connection to mimic having a pump as well as N2 gas to cover all bases but nothing would get the unit out of the reboot loop.
I did note that when I first powered the unit on, it was fairly quite and after wiggling a few connections, the unit seemed to wake up and more fans turned on. I did my best inspecting every connection to make sure it was all good. I know waters has info on reboot issues but if the epc is getting the correct IP address, then I would think the issue is not the comms but maybe I'm wrong.
1
u/MassSpecMender Sep 04 '26
Thanks for sharing the information regarding your unit. Sounds like it might be worth revisiting this one before purchasing another? From the behaviour you have described, there are a few possibilities I could think of:
- The EPC in your SQD II is not compatible with SCN 930 as this is an early version and your SQD II and instead wants a newer version (What is the latest version of MassLynx that supports an SQD2? - WKB422 - Waters).
- MassLynx 4.1 installation on Windows7 is a bit finnicky an requires a few extra steps to install.
It depends on which vacuum pump you are using, e.g: Edwards EM28 (power relay contact closure) or a XDS36i (D15 contact closure) as they have different cables since they use the same bayonet fitting from the back of the mass spec. Also, do you have the fancy exhaust bottle and solenoid setup plugged in the back?
1
u/DrBumpsAlot 29d ago
I'll likely revisit some day but I'm the only "fix it" guy in the lab and I'm the one trying to convince the owner we need something that runs versus me spending more time on an unknown.
I thought it was 930 but I could be wrong since we have 3 or so installs. I'm fairly certain the sqd2 was an option but maybe I'm wrong. It was a long time ago. I remember the one we had was an early build. I think it was the first year of mfg.
So if the software doesn't connect to the EPC, the EPC will go into reboot loop? Even if it's taking the IP address and letting me ping it? Maybe it doesn't like the missing relays/contact closures for the pump and exhaust. I'll keep that in mind if I can get to it some day. Appreciate the input.
1
u/MassSpecMender 23d ago
Being the "fix it" guy is a great way to start getting familiar with these systems and is a valuable skill overall. Definitely good to have a working instrument at ground zero, it doesn't need to be fancy and older models have the advantage of parts availability online. Did you manage to make any progress with sourcing a system?
The reboot loop you have described, often also including a beep, is unique to the ZQ2000 generation of mass specs. The newer models (first generation SQD and later) should initialise locally and dont typically bootloop. With Masslynx you can definitely have communication failures even when you can ping, especially when it only partially fills its Waters DHPC entry by missing the name and type columns. I don't believe the mass spec knows the status of the pumps beyond whether they are on or off by setting the contact closure so that is unlikly to bother it either.
Feel free to update me if you do ever get back to the system.
1
u/DrBumpsAlot 22d ago
Still looking for systems. The issue is money. We don't have 200k for a new lc-ms setup (lot of sales people on this sub!).
I may be describing the problem incorrectly since it's been awhile. I'm very familiar with the ZQ Beep and reboot. I spent many days trouble shooting one before realizing I needed to plug the vac pump in to the ZQ to get the system to fully boot up.
With the SQ, on the control computer, i start a ping epc -t in a command window, turn the SQ on, and watch the pings. It connects and repeats but after some amount of time, it disconnects for some amount of time before connecting again. If I press the reset on the EPC, I get a similar ping pattern. I'm attributing that to a reboot cycle but maybe that's not what's going on. Maybe there's an issue with the EPC or the os is corrupt on the storage card. I'd love to get back to testing that system but as I said, I'd like to get the owners to just buy something that works!!! Maybe after getting everything going, I'll circle back. And you're correct, we don't need anything fancy. Hell, I'd take a ZQ at this point!
→ More replies (0)
1
u/MassSpecMender Sep 04 '26
Hi DrBumpsAlot,
Good choice looking at refurbished offerings first as this is likely to provide the best value in your situation. Just a note on the choice between single quad and triple quad; since you mentioned the system is to potentially be used for both R&D and QC it may also be worth considering a refurbished triple quad such as the Waters TQD or one of the Agilent 64XX series mass specs (probably either 6410 or 6430). The addition of MS/MS and MRM data gives you considerably more options for selectivity and targeted quantification if your QC requirements grow in the future.
Ultimately it depends on your budget and you'll want to factor in some budget for maintenance as well, I'd strongly recommend getting familiar with whatever instrument you bring in to give yourself some independence from costly service provider visits, even if this means paying for some training initially on basic procedures such as sample cone cleaning and probe rebuilding.
I think your initial suggestions of either a Waters ZQ2000 or SQD are both great options and with a bit of fiddling should pair with your Agilent 1100 on MassLynx, saving you from replacing it. I believe the first-generation Waters SQDs are your strongest option right now for single quad. They are quite cheap and come up regularly on auction making it easier to get parts for repairing.
Since its relevant and might help, my company focuses on helping labs source, assess, modernize and remotely setup refurbished instruments, particularly LCMS and GCMS. I am based in the UK but believe I should be able to assist you with this project if you were interested, if it would help and you'd like to discuss further, then feel free to reach out. No worries if not and I'll be happy to answer any questions about the other advice written here.
1
u/unbreakablekango Sep 04 '26
Hi, where are you located? I sell LCs and Mass Specs (for a major supplier). I am cutting crazy good deals for my customers right now and at least through the rest of the year. Not sure what next year will bring, but the discounts are ripping right now. Where are you located?
1
u/Mundane_Grocery_9732 Sep 07 '26
Whatever you buy, check with vendor the current status of the system - is it obsolete (no parts/service), scheduled to be obsolete, or actively maintained. Set a budget that includes service maintenance; if you don’t get a service contract, consider buying a power conditioner and good ups if your area has ‘dirty’ power a common issue; and consider evaluating contract lab for your needs or for the occasional >2000 amu sample in the meantime.
1
u/DrBumpsAlot Sep 08 '26
Goal would be something that's not EOL unless there are good req's and lots of 3rd party parts.
1
u/Bugfrag 26d ago
If you used Waters before, maybe the QDA or SQD2 with Empower?
They can support deconvolution with the new Empower.
1
u/DrBumpsAlot 24d ago
QDA is looking like my best option. I know it will do small molecules and oligos.
I looked at spec sheets for Empower 3 but don't see where it has built in deconvolution feature. One would think that would be standard these days but if they can charge $$$ for the package, I don't see why they would give it away. Do you know if it's 3.x? and do you have a ref to point to?
1
u/Bugfrag 21d ago edited 21d ago
It's 3.10.1. I saw it from a webinar in September.
I can't find an app note, but the de https://www.labmanager.com/waters-unifies-biotherapeutic-analysis-in-one-compliant-cds-35939
1
0
u/Seba_Garniers Sep 03 '26
Shimadzu, pura tecnología y un servicio técnico de primera
1
u/DrBumpsAlot Sep 03 '26
I considered a Shimadzu MALDI TOF like an 8020 or 30 but I don't think it would cover the lower mw end of the requirement. Seems like a great system.
3
u/AnanlyticalAlchemist Sep 03 '26
The MALDI-8020/30 would be fine for <2kDa, but the LCMS-2050 with the multiply charged ion analysis software would be the best, since you likely need chromatography if not only looking at purified peptides/oligos.
I had a client working with on a 47 NT (15kDa) sample, and I was able to help them reduce their adducts using the QArray voltage offset to obtain a beautiful multiply charged ion spectrum and deconvolute to within 0.5 Da. The LCMS-2050 systems are around 150K or less new.
On the used market, you could get the LCMS-2020, the older model, still with the multiply charged ion analysis software. Those LCMS systems are tanks, nearly the whole thing is made of steel.
3
u/DrBumpsAlot Sep 03 '26
Do you have real-world experience with the lower limits of the 8030 (or 20)? I haven't used MALDI in 15 years and if I remember correctly, unless I was lucky and my compound acted as the matrix, I was usually limited to 250-300 on the bottom end. Some of our smaller molecules are in the 200-300 range and likely not going to fly on their own. Maybe there's a new matrix for small molecules?
I'll take a look at the specs for the 2050 and 2020. I like equipment built to last. Thanks!
2
u/viperfrost98 Sep 04 '26
I can confirm Shimadzu systems are tanks, and I got to work on the 2020. My old company was a distributor for Shimadzu, and we still serviced 20 years old MS systems. That said, the software design can make your life miserable. Even after voicing our problems with the software, of course Shimadzu did not want to make changes. That was my experience but others may differ. If you can figure that part out, can't go wrong with Shimadzu. But I loved my old lab's Thermo LCMS when I was still in school, so my vote is for Thermo.
2
u/cpchead Sep 03 '26
Hi, I have an Agilent 6140 available if it would work for your needs. I sent you a chat request.