Sciencemadness Discussion Board - Advice on buying a GC/MS

Advice on buying a GC/MS

nleslie321 - 18-5-2020 at 00:53

So im hoping to get a GC/MS off ebay for around $2,500 to $4,000 seen some in working condition with pump etc for that price. im weighing up between a GC/MS and an IR Spec at the same price. What are the pros and cons of each? I will be using them for identifying/confirming chemical intermediates, impurities and finished products in synthesis in a home lab. Im only in the second year of my chemistry degree at uni and have not had much hands on except for basic operation with either IR spec or GC/MS machines. I have 7 years of self taught lab experience also before starting study. im leaning towards GC/MS as its the gold standard in identifying compounds but as its more complex than the IR Spec im worried it will be a lot more of a big hassle if it breaks down rather than the IR spec.
Any guidance would be great.

[Edited on 18-5-2020 by nleslie321]

Ubya - 18-5-2020 at 02:15

go for GC/MS, if you want to know the compounds of a mixture that is the easiest way, with IR you just get a sum of all the active groups of your sample.
after a synthesis if you want to check for example the purity of your product you could make an IR spectrum and look for not expected bands. if your product is an alcohol and you see a C=O band you know something is wrong, but you won't know what's the impurity.

with CG/MS you get the separation of a mixture thanks to the GC, and then you can make a mass spectrum to see which peak is your product for example.

plus IR has a different sample preparation depending on the state of your sample, if it is a pure liquid, a solution, or a solid.
in gas chromatrography you just need to be sure about the volatility of it.

Syn the Sizer - 18-5-2020 at 03:26

Honestly I was thinking IR was the way to go but after reading Ubyas opinion I fully agree with them. GC/MS is the way to go, just because GC was the most boring class doesn't mean it's useless.

Nonexistent - 18-5-2020 at 04:00

if I could get a gc/ms or hplc for that price in good working condition, I definitely would do so. You could also start some form of basic testing and make an income from it. As Ubya said IR is just groups, great for seeing if you have your compound, and purity, but gc/ms and once you have a method, you have a nice separation and %'s, + your ms library of compounds, so many things you could look at and discover.

Metacelsus - 18-5-2020 at 05:25

GC-MS is better, but the maintenance and operating costs will be higher. With IR you don't need gas cylinders or fancy pumps.

VSEPR_VOID - 18-5-2020 at 05:57

I would recommend buying a visible light spec. They are cheap and will be able to identify any compound you prepare that is colored. They also are easy to upkeep, and you only need to buy new kimwipes. I really like using them. Nanodrops are too easy to fuck up.

A GC will require an expensive mobile phase. Hydrogen and helium are both expensive. If the machine breaks, good luck fixing it. However, if you do buy one, pay special attention to what sort of columns it uses and can accept. If you clog one up, or cant get a sample to elute, you would have to buy a new one.

Also, you can use a DIY syringe pump to send your product through a chromatography column, and measure each fraction with whatever you buy

Ubya - 18-5-2020 at 06:58

Quote: Originally posted by VSEPR_VOID

I would recommend buying a visible light spec. They are cheap and will be able to identify any compound you prepare that is colored. They also are easy to upkeep, and you only need to buy new kimwipes. I really like using them. Nanodrops are too easy to fuck up.

A GC will require an expensive mobile phase. Hydrogen and helium are both expensive. If the machine breaks, good luck fixing it. However, if you do buy one, pay special attention to what sort of columns it uses and can accept. If you clog one up, or cant get a sample to elute, you would have to buy a new one.

Also, you can use a DIY syringe pump to send your product through a chromatography column, and measure each fraction with whatever you buy

most organic compounds are white powders, so at least an uv-vis is necessary, plus if IR just shows functional groups, UV-Vis just shows conjucated pi systems and a few low energy orbital transitions, so identification is even harder.

a GC/MS no doubt has a higher maintenance cost, but the amount of informations you get is way higher than other techniques.

hydrogen and helium could be substituted with a nitrogen generator, we used that in my university for the lower tier instruments.

there's no better instrument in absolute, it depends on what informations you want to get from it, uv-vis is the cheapest option, you can buy one from ebay for 200 dollars, IR needs special cells depending on the sample and it is not great at analyzing mixtures, CG/MS you get separation of complex mixtures from the CG, and then you get a mass spectra that you can read yourself or match with one from a database and get a better idea of your compound/impurity.
next is getting a 300MHz superconducting NMR c:

Dr.Bob - 18-5-2020 at 18:47

For small molecules, a GC/MS is a great tool. If you can get a FID or thermal detector, that will help even more, as some molecules do not ionize well. GC is a powerful tool for checking the purity of a molecule, it can detect amounts to several orders of magnitude to get purities to a high precision. And depending on the detectors, some are very universal. The MS is the part most likely to give issues, but the ones on GS are simpler than any other type in my experience. But they will take some work to perform.

RogueRose - 18-5-2020 at 19:41

I've been considering getting something to do this for awhile as my goal is to be able to test the purity of compounds and see what the impurities are. I'd also like to be able to test water samples to see what contaminants they have, and I'm wondering if GC/MS is the best option for this.

The biggest question I have with the GC/MS is the database that is needed to make the comparison between the sample and the known compounds. Are these database's freely available, do they come with the machine or do you have to buy them or subscribe?

I've seen a number of machines sold with I guess what are called "columns" which look like small diameter metal hoses with a screw connection on each side and they vary in length. I see that they are really expensive when new but often see them sold, used, in lots for pretty low prices (like 5-10% of new price, sometimes lower when a large lot). How many of these do you need and what are the differences in them? Keep in mind IDK the full process of this, I've never done it myself, so any explanation I'm grateful!.

So i see that people listed H2 and He as consumables needed for GC/MS, is there anything else and does it have to be a special gas, like ACS grade, or can it be purchased the same as gases from welding suppliers? I also thought that methanol is used in this or is that for LC/MS? Are there any other consumables that are needed?

Does anyone know what the average cost would be to run a sample - meaning what the cost is of consumables?

As for the pump, is this for vacuum or to push the solution through the tube?

Ubya - 18-5-2020 at 22:30

Quote: Originally posted by RogueRose

I've been considering getting something to do this for awhile as my goal is to be able to test the purity of compounds and see what the impurities are. I'd also like to be able to test water samples to see what contaminants they have, and I'm wondering if GC/MS is the best option for this.

The biggest question I have with the GC/MS is the database that is needed to make the comparison between the sample and the known compounds. Are these database's freely available, do they come with the machine or do you have to buy them or subscribe?

I've seen a number of machines sold with I guess what are called "columns" which look like small diameter metal hoses with a screw connection on each side and they vary in length. I see that they are really expensive when new but often see them sold, used, in lots for pretty low prices (like 5-10% of new price, sometimes lower when a large lot). How many of these do you need and what are the differences in them? Keep in mind IDK the full process of this, I've never done it myself, so any explanation I'm grateful!.

So i see that people listed H2 and He as consumables needed for GC/MS, is there anything else and does it have to be a special gas, like ACS grade, or can it be purchased the same as gases from welding suppliers? I also thought that methanol is used in this or is that for LC/MS? Are there any other consumables that are needed?

Does anyone know what the average cost would be to run a sample - meaning what the cost is of consumables?

As for the pump, is this for vacuum or to push the solution through the tube?

oh boi many questions, i'll try to explain my best.
there are tons of MS databases many for many you need to buy a pricey subscription, others are free but have less data. my mass spectroscopy professor explained to us how they work (i haven't had the occasion of using one myself), a mass spectra heavily depends on the instrument, most of the databases use electron ionization mass spectra as they give the most reproducilble data, different combinations of ionization sources and detectors will give you a different spectrum. so each database is not universal, you need to pick the one best suited for your instrument.

the columns. columns are used in the CG part of the instrument, they "simply" are a tube with something inside, when the carrier gas with the analyte flows through it, the different interactions of the compunds with the stationary phase (the thing inside the tube) will gradually separate them. the only way to change the interactions of the sample with the stationary phase is 1) change the nature of the stationary phase (change column) or 2) change the temperature (higher the temperture the faster the interactions with the stationary phase) or 3) change the flow of carrier gas.

gas chromatography columns can be packed or capillary (there are more types but this two are the broadest)
packed columns are usually stainless steel tubes of a few mm in diameter filled with an adsorbant or a support material covered in a liquid film (so solid-gas interactions or liquid-gas interactions)
capillary columns are thin, like micrometer thin tubes of silica covered with a liquid film inside.
how many columns do you need? it depends strongly on the type of analysis you want to perform. every column has different stationary phases with different polarities and different interactions with a family of substances. so to get the best possible separation you need the best suited column (and temperature and flow rates xD)
for example one of my many projects is building a gas chromatograph, i just need to check hydrocarbons so i found i could make my own media for a packed column covering some silica gel powder (80-100 mesh) with a layer of paraffin wax.

the difference is that some give better results with a class of compounds and give shitty separations with another class, so it depends on what you are testing.

yes the carrier gas for gas chromatography must be pure, like 99.995% pure or more, a welding supplier won't work
consumables are: the inlet septum, after many injections it starts to leak,
the graphite ferrule holding the capillary column (it should be changed every time you change a column but maybe you can keep it as we are not aiming for extra precise data), the detector also has consumables, a GC/MS has a mass spectrometer as detector, but if you only want a gas chromatograph you need to pick a detector, for example a FID (flame ionization detector) needs high purity hydrogen to work, TCD (thermal conductivity detectors) use heated filaments and like any incandescent light bulb they can burn.
yeah methanol is usually used to dilute the sample before injection, and yeah, heet methanol won't be good enough xD

the cost is pretty relative, universities buy everything from Sigma so prices are not low, but it also depends on the instrument. if you use a packed column, with N2 as carrier gas (from a nitrogen generator so no high pressure tanks), with a TCD detector(an universal detector) you can run an analysis for pennies, but then if you use 7N helium as carrier gas with a chiral column and a nickel-63 electron capture detector wee ohh costs are over the roof.

push. if you have a gas cylinder you just use a regulator, i mean 1 from the tank, and another fine tuning-pc controlled regulator before the inlet

nleslie321 - 19-5-2020 at 03:56

after reading all the comments i think im going to get a GC/MS. What about LC/MS is that similar in usefulness to GC/MS. I can get ultra high purity hydrogen gas bottles delivered to my house for carrier gas for GC/MS and i will buy one with the vacuum pump included. I am hoping to find someone on here that has a copy or can get me a copy of the software needed for the GC/MS. I can buy high purity carrier solvents from chemical supply near me also. What about the columns that were talked about? do i need to worry getting different ones for testing different types of substances?

DavidJR - 19-5-2020 at 04:36

HPLC is overall just much more versatile than GC. You have more options of separation modes, and you aren't limited by the need for analytes to be volatile and generally there is no need for derivatization.

nleslie321 - 19-5-2020 at 04:48

You think HPLC is more versatile than LC/MS or GC/MS?

Dr.Bob - 19-5-2020 at 05:30

Straight HPLC (using a UV or RI detector) is good for determining what componnents are in a mixture, and comparing a compound to a starndard for identification. But without a MS on it, it will not tell you anything about the identity of the components. It is the liquid version of a GC.

The costs of running each will be similar, as a GC requires a carrier gas, either helium (which is getting pricey) or hydrogen (dangerous, but cheap). For FID detector, H2 is needed. For an HPLC, you will need solvents, usually water and an organic, typically methanol (cheap) or acetonitrile (pricey), both can work OK. Both GC and HPLC require a column of some sort to separate components into peaks for detection, most columns are expensive.

Any MS, whether on an HPLC, or a GC, will be somewhat expensive, hard to maintain, and require a very good vacuum pump. So the difference between GC and HPLC is that GC is mostly ideal for compounds that volitalize at some temp below 200 or so (typically liquids or organics with low mps), but HPLC works best for larger mw liquids and most solids. If you don't know what each is good for, then buying one might be a bad idea, unless you have a lot of time and money. All of these tools are great for doing analytical work, but each has its costs and limitations. While I have heard of a few individuals buying these, even many small chemical companies can't afford to buy or use them, due to the operating costs.

DavidJR - 19-5-2020 at 05:55

Sorry, I was strictly just talking about the chromatography part... Obviously HPLC/MS is much more useful than HPLC/UV. But HPLC/UV is undeniably more versatile than GC/FID etc, and HPLC/MS is similarly more versatile than GC/MS. GC has its place, of course, but if I had to choose one, it would be an HPLC. (In fact, I did - I have an HPLC in my garage, but no MS (yet)).

Ubya - 19-5-2020 at 05:56

another thing, all of these instruments are not "plug and play", every analysis is different from the others, and to get the best (or even just usable) results you need to tweak many factors, just installing the right column and pressing the start button is not nearly enough.
to run a CG or an HPLC you need to be very familiar with the van deemter equation, because by looking at the spectrum you can then modify the temperature/flow rate/eluent to get good separation.

then you are adding a mass spectrum instrument to it, i think that most machines you can find on the web at a low enough price are quadrupole mass spectrometers.

then another thing, HPLC/MS and GC/MS interfaces are different. while GC/MS can use an electron ionization source, HPLC uses elelectrospray ionization.

problem solving also is not easy without training, how do you know that your column is at the end of its life? how do you know that a bubble in the HPLC is messing with your specteum? did you degass your solvents?

the base principle of each system is not hard at all to understand, it's the many many little things that can mess your spectrum, so my advise is before buying anything, HPLC, GC, HPLC/MS, GC/MS and all the flavours of systems with different detectors, analyzers etc etc, study well the theory behind to understand well what each can do, because you need that angway to run the instrument.

i know you expect us to just say "buy that it's better" but honestly there isn't a better, each one has its pros and cons, only you know what you need it for, and by understanding what each is capable of you can decide accordingly.

Nonexistent - 19-5-2020 at 07:28

Quote: Originally posted by RogueRose

It really comes down to a matter of what you want to test. GC for compounds that are volatile, HPLC for most things, but For water (especially from pools, ponds, etc), I'd go for a Flow injection analyser, the salts and potential metals would destroy a GC column and also over time ruin hplc columns.

Quote: Originally posted by RogueRose

The biggest question I have with the GC/MS is the database that is needed to make the comparison between the sample and the known compounds. Are these database's freely available, do they come with the machine or do you have to buy them or subscribe?

There are free ones available, but smaller databases, you can of course buy/subscrive to a company for larger and more often updated ones.

Quote: Originally posted by RogueRose

I've seen a number of machines sold with I guess what are called "columns" which look like small diameter metal hoses with a screw connection on each side and they vary in length. I see that they are really expensive when new but often see them sold, used, in lots for pretty low prices (like 5-10% of new price, sometimes lower when a large lot). How many of these do you need and what are the differences in them? Keep in mind IDK the full process of this, I've never done it myself, so any explanation I'm grateful!.

I don't know how game I would be to use 2nd hand columns, if they were still working well, they'd likely be kept, unless the company shut down/was no longer doing that form of testing. But I'd still be wary, an old column can have many problems, pressure being too high, missing overlapping compounds and not having clean peaks for example.

Quote: Originally posted by RogueRose

Does anyone know what the average cost would be to run a sample - meaning what the cost is of consumables?

That all depends on the type of sample you want to run. Your mobile phase, any derivitizarions, sample preparation, all adds up and all varies from one test to another.

Quote: Originally posted by DavidJR

but if I had to choose one, it would be an HPLC. (In fact, I did - I have an HPLC in my garage, but no MS (yet)).

So jealous, I'd be putting all sorts of stuff through, what do you mostly run through it?

Quote: Originally posted by nleslie321

You think HPLC is more versatile than LC/MS or GC/MS?

if you have the space and money, LC/MS

DavidJR - 19-5-2020 at 16:40

Quote: Originally posted by Nonexistent

I've actually had pretty good luck with second hand C18 columns. I think part of that is that there are a lot of regulated labs that have to replace columns as soon as they start showing any sign of degraded performance - but that doesn't mean the column is not usable any more.

It's worth going through a cleaning process, cycling through progressively more non-polar solvents and back, just to make sure anything strongly retained is flushed out. I.e. methanol, acetonitrile, isopropanol, dichloromethane, hexane, isopropanol, methanol (10 column volumes each).

Quote: Originally posted by Nonexistent

So jealous, I'd be putting all sorts of stuff through, what do you mostly run through it?

Depends what I'm working on at the time! Mostly using it for reaction monitoring. But I also was doing air analyses for aldehyde pollution with 2,4-DNPH (on hold due to coronavirus situation meaning I can't go out and take samples).

[Edited on 20-5-2020 by DavidJR]

Bmoore55 - 19-5-2020 at 17:33

I currently work with both and if you want something that has much less maintenance to mess with go for the IR. IR is useful for identifying most organic intermediates and a good rule of thumb with regards to identifying a material is A) the thing you are looking to analyze should have as little water as possible since that strongly absorbs in the MID IR range and B) the concentration of what you are interested in should be at least 5% in most cases to even have a chance of identifying. Don't get me wrong GCMS is an amazing tool and if you have the skills to do the regular maintenance properly and you can afford the parts and software then it is also a great tool. I just find that a great compliment to anyone doing chemistry is a relatively quick and easy analysis, and when I think quick and easy I think of IR. Just for your reference I am currently running and Agilent GC 7890 and mass spec 5975C and I currently have two Perkin Elmer Spectrum 100 FTIRs.

DavidJR - 19-5-2020 at 19:00

I often see old FTIRs sell on ebay for more than old HPLCs...

nleslie321 - 20-5-2020 at 04:00

what about something like this? https://www.ebay.com/itm/Varian-CP-3800-3800-Saturn-2000-MS-...
or i was looking at an IR spec like this https://www.ebay.com/itm/THERMO-NICOLET-IR300-SPECTROMETER-W...
I think after a lot of thinking im going to go with a IR Spec learn that inside and out then look at buying a LC/MS in a year or so.

Ubya - 20-5-2020 at 06:30

Quote: Originally posted by DavidJR

I often see old FTIRs sell on ebay for more than old HPLCs...

eh but they usually don't have a PC controller, they have a roll of paper where the spectrum is drawn by the instrument, it could still be used, but having to measure peaks and bands like 40 years ago with a caliper mh

monolithic - 20-5-2020 at 07:31

I've always wanted to buy HPLC or GC/MS but the learning curve seems absurdly steep. So much to go wrong with the equipment, concerns about proprietary software, and so much to learn just to set it up. Then even more to learn when it comes to keeping it running and tweaking things to provide usable data... and then learning to actually interpret the data.

DavidJR - 20-5-2020 at 08:41

Quote: Originally posted by monolithic

I've always wanted to buy HPLC or GC/MS but the learning curve seems absurdly steep. So much to go wrong with the equipment, concerns about proprietary software, and so much to learn just to set it up. Then even more to learn when it comes to keeping it running and tweaking things to provide usable data... and then learning to actually interpret the data.

Yeah, it can definitely be a bit of a time and money pit... But I think it's worth it.

Bmoore55 - 20-5-2020 at 15:04

Be weary of buying an FTIR that is sitting in what looks like a garage or a storage area. Often the optics are KBr windows that get destroyed with high moisture and can make your purchase a bust.

nleslie321 - 20-5-2020 at 21:12

Im only looking at ads on ebay for ir spec that say working condition so i can get a refund via paypal if its damaged. The one i linked has ATIR accessory with it thats worth a fair bit by itself. Im thinking of getting that one im just going to wait another couple of weeks to see what else comes up for sale.

RogueRose - 21-5-2020 at 09:30

IDK know what kind of chromotographi it is, I've seen it called an HPCL well as a GCMS, so I'm at a loss here. These units look to be in good shape and the price is VERY attractive, though I think it will take an 1180 miles drive to get there b/c shipping will be a PITA and just as expensive....

Would this unit be good for identifying compounds (purity and contaminants) as well as
doing water samples of what is in the water?

Thermo Finnigan LCQ Advantage Model: LCQ Advatage Mass Spectrometer Sysytem
Thermo Finnigan Trace DSQ, Model: Trace DSQ-Mass Spectrometer,
Thermo Finnigan Autosampler Surveyor, Model: Surveypr Autosampler

Thermo Finnigan LCQ Advantage Model: LCQ Advatage Mass Spectrometer Sysytem

https://www.ebay.com/itm/Thermo-Finnigan-LCQ-Advantage-Mass-...

https://www.labx.com/product/thermo-lcq

http://www.myco-analytical.com/product/thermo-finnigan-lcq-a...

Thermo Finnigan Trace DSQ: Trace DSQ-Mass Spectrometer

https://www.bostonind.com/thermo-finnigan-ltq-ion-trap-mass-...

https://www.ebay.com/i/183928826777?chn=ps&norover=1&...

Thermo Finnigan Autosampler Surveyor, Model: Surveypr Autosampler

https://www.ebay.com/itm/Thermo-Scientific-Finnigan-Surveyor...

https://assets.thermofisher.com/TFS-Assets/CMD/Specification...

[Edited on 5-21-2020 by RogueRose]

DavidJR - 21-5-2020 at 15:19

Rogue rose: that is just a mass spec, no chromatograph there. So it will really only be useful for things that are already pure, and much less useful for mixtures.

Ubya - 21-5-2020 at 21:57

Rogue, your question is really generic

Quote:

Would this unit be good for identifying compounds (purity and contaminants) as well as
doing water samples of what is in the water?

the first 2 instruments you posted are only mass spectrometers, the one from ebay even lacks the injection pump. the third is an autosampler, alone is useless and you don't need it anyway.

please describe exactly what do you need an HPLC/MS for.
identifying purity and contaminants is too broad, are you looking for molecules big as proteins or polymers? or are you looking for metal ions? Mass spectrometers are not magic genie, they have limits, most of them won't show you metal ions, while a GC with an atomic emission detector easily can.

most of the sales on ebay don't have the software with the instrument, i know that there are some custom softwares that can interface with the instrument, but not all of them are capable of this, and without the 10k software license, you would have an expensive and bulky paper weight.

i know you are tempted to buy a shiny big instrument, but seriously, study before buying anything, you need knowledge of the entire process to see what (or if it) fits what you want to do.
there isn't only one kind of mass spectrometer each one can have different types of ion source/analyzer/detector, and the combination of these decides what you can do with it.

you could spend 1Mil for an FTICR, but if you use it to test lead in water you won't see much, is it bad? no it's just made to see high mass molecules.
i would gladly give you the material i used to study at university, but it is a mix of italian and english, to begin you can just dive on wikipedia and read everything you can about mass spectrometry, liquid chromatography and gas chromatography, only later you can decide. we are here to help but right now it is like you are asking us what's the best car to go to nord of the US and you are showing us a sports car, a lada and a trailer without an engine

nleslie321 - 21-5-2020 at 23:38

ive spoken to the seller and this is said to be completely working in good condition. I know how to use and read IR spec from classes at university. All im wanting is someones opinion on if its worth that price and am i likely to have any problems or things that will be worn out. i have the software already for this also. my main use will be identifying end products from organic synthesis making sure i got what i was intending to synthesize.
https://www.ebay.com/itm/THERMO-NICOLET-IR300-SPECTROMETER-W...

[Edited on 22-5-2020 by nleslie321]

Mateo_swe - 24-5-2020 at 11:34

In the country where i live, when a company has gone bankrupt they have these auctions with all kinds of gear and machines from the fallen company that is offered to highest bidder.
In these auctions there sometimes is lab gear and advanced lab machines up for sale.
Thats a good place to look if you have similar auctions where you live.
Sometimes very advanced gear is sold for fractions what they are actually worth.

Ubya - 24-5-2020 at 15:30

Quote: Originally posted by Mateo_swe

In the country where i live, when a company has gone bankrupt they have these auctions with all kinds of gear and machines from the fallen company that is offered to highest bidder.
In these auctions there sometimes is lab gear and advanced lab machines up for sale.
Thats a good place to look if you have similar auctions where you live.
Sometimes very advanced gear is sold for fractions what they are actually worth.

i tried to look its specs but i could only find that the latest opereting system it supports is windows XP and that it can analyse solids and liquids. do you have some specs of this instrument?

beerwiz - 29-5-2020 at 00:29

Get an FTIR with ATR. Most models come with software that can do a compound search, meaning it can identify multiple compounds in a sample provided that you also buy the database.

nleslie321 - 31-5-2020 at 19:43

I bought the model i posted a link to above, all up with shipping and tax $3000 Australian. I have the Omnic software already so now just waiting until it gets here.