GC/MS, GC/MS/MS or GC/MSn

[yanner]

Hi!

I am new here and I hope to read some of your opinion. I am buying a new GC/MS system, but I have different possibilities and now I’ve become headache because I can’t so easily choose one. I know that when I buy the Agilent 5975C system I have a very good tool but I’m hoping to rise the sensitivity by buying a GC/MS/MS system (Varian 300-MS TQ) or a GC/MSn with ion trap (Varian 240-MS/450-GC System or Finnigan PolarisQ). I only have one problem… I’ve never worked with an ion trap and I’m not sure if I can handle the problems which are connected with this kind of GC/MS. Can someone tell me if I can easily use the PMW libraries (they were made with a single Quad GC/MS)… are the proportions of the MS signals like in a single Quad GC/MS? When you have other propositions… my ear is open. I would be very grateful if someone has the possibility/experience to compare this different systems and producers. I’m very curious which experiences you made. Thank you for your time… unfortunately this text is very long .

[Don_Hilton]

If you are going to use libraries - I assume that you are going to analyze unknowns. For unknowns and sensivity, also include GC-TOFMS in your list of instruments (I can think of two vendors) to look at. While you can get very high sensitivity for target analysis with SIM mode in a quadrople or a GC-MS/MS system, TOFMS offers sensitivity with acquisition across a wide mass range and at acquisition rates sufficiently high to get good results from spectral deconvolution.

[Ron]

If you are using libraries for compound identification you should stick with a single quadrupole instrument in most cases. A TOF or an external ionization mass spectrometer will give similar mass spectra, but if you can have only one mass spectrometer a single quadrupole instrument is usually the preferred choice.

[yanner]

Thank you for your answers… but how does it look like with the ion trap (internal ionization). Can I easily use the libraries? Can I use the ion trap for as successful compound identification as with the quadrupole? Can I really obtain better sensitivity with the ion trap in the routine analysis? When I need a system that I would call more or less universal is the ion trap a good choice?

[Don_Hilton]

From the folks that I have talked with, the ion trap is very good for sensitivity for some specific target analyses. Spectra often show significant differences from the libraries obtained on other instruments.

If you are going to obtain an instrument, take a couple of samples that are typical of the work you will be doing and ask the various vendors to show you how well the instrument will do in solving the kinds of problems you have. If you want to solve unknown compounds, I would suggest that you take a known mixture and treat it as an unknown - then you will know if the answer is right. Look at thins like correct identification of peaks when they coelute or ability to quantify a minor component in a mixture when it coelutes with a compound that is present at high concentration (this can give an ion trap problems).

Have the vendors give you references of instrument users who do similar work to you so you can 1) find out how the instrument works for them and 2) you will have a contact who may be able to help you out in the future.

On Ron's comment of the quadropole being the instrument of preferred choice - for many it is. I have a TOF and for the work I am doing, and it is doing things a quad could only dream of. Bottom line - get the instrument that matches the task you have for it. (And, I've run quads and loved them too.)

Look at the various vendors -- sometimes the service available in one area makes one instrument preferable to another.

[Ron]

It has been a while since I have used an ion trap, but there were differences in the mass spectra of many compounds. There was a function in the library search that you could turn on that was supposed to improve library matches by mathematically manipulation of the mass spectra.

If you want a classical mass spectrum to match against libraries I would go with a simple single quad instrument. They start in the low $50K range for a system, so there is not a huge difference in price between a low end quad and a low end trap. If you want good library matches on a trap you need an external ionization trap.

[tima]

You need to talk to ion trap users. I have used both and the most recent purchase that I was involved with had me insist we get a quadrupole over an ion trap. I hate to name the manufacturer but be aware that they were purchased by Agilent.

The most pressing problem I had was from an old ion trap that had problems with "space charging". Put simply, because of the design of the ion trap, neutral gas molecules will and can cause proton transfer from the neutral to the ions. This is especially problematic with aliphatics or any straight chained alcohols or other types of organics. The aromatics are fine. What happens is your molecular ion will be M+1. So for hexane that has a moelcular weight of m/z of 86 you will see a m/z 0f 87. They said it only happend at high concentration levels so all you had to do is dilute the sample. Forget about it! This can have serious implications especially if you are using the instrument for legal samples. The specialist that I consulted said you should see it as a feature...BS. The instrument is now unplugged and our 5973 is our work horse. Timothy

[tima]

I forgot to ask...what are the sensitivity claims for the the ion trap vs the quadrupole. We ran our 5973 (updated electronics and ion source parts) for PAH's and I saw 100 femtograms (on the column) easily. This shocked me. I had to go back a check my caliculations and dilutions. IT WAS REAL. So let me know.

[Ron]

The last time I checked specifications the claimed sensitivity for an ion trap was a signal to noise ratio of greater than 70:1 for a 1 pg injection of OFN. Quadrupole instruments claim a signal to noise of 150:1 to 400:1 for a 1 pg injection of OFN.

One point to remember is that an ion trap can hold only a certain number of ions, so there are sensitivity issues in a complex matrix with ion traps. In a complex matrix a quad or TOF will perform much better than an ion trap.

[yanner]

So the Ion trap should have the external ionization mode when I want to have a chance to use libraries. And when I will analyze complex matrices is a single quad better because in an ion trap I can have problems with sensitivity. When I am looking at your posts I can make only one conclusion: I should buy a GC/MS/MS. Then I can use it to work in a scan mode like a normal single quad (and use libraries without problems), I won’t have problems with complex matrices and for more sensitive applications I can use the second quad. Am I right?

[tima]

Hello Yanner,


....So the Ion trap should have the external ionization mode when I want to have a chance to use libraries....

You can use MS libraries with ion traps (NIST05, Wiley or NBS databases) because in most cases, the ion trap produces classical mass spectra. You just have to operate the ion trap in the scan mode. Simple.


....And when I will analyze complex matrices is a single quad better because in an ion trap I can have problems with sensitivity....


From what I remember one of the claims to fame with ion traps is their sensitivity in the full scan mode. It could match the sensitivity of a quadrupole instrument operating in the most sensitive mode (S.I.M.). I think ion trap problems can be real if your sample matrix is high. For example, lots of column bleed or an envelope of aliphatics and you are testing for a pesticide in the middle of the chromatogram containing co-eluting aliphatics.


When I am looking at your posts I can make only one conclusion: I should buy a GC/MS/MS. Then I can use it to work in a scan mode like a normal single quad (and use libraries without problems), I won’t have problems with complex matrices and for more sensitive applications I can use the second quad. Am I right?

A GC/MS/MS is new on the market and I think its most likely much more expensive than a single quad. The only reason I can think of having one, is for target analyses. This will afford you good selectivity and low S/N even with high sample matrix or possible interferences.

What are your applications? VOC's, pesticide analysis, pharmaceuticals???

[Ron]

The type of instrument you need depends on what you want to do. Traps have certain advantages, TOFs have certain advantages, triple quads have certain advantages, as do single quads. An important thing to remember is that all these types of mass specs also have disadvantages. You need to match the instrument to the application. For example, I have seen biological extract samples that heve relatively high levels of the target analyte, but there is so much matrix interference that a triple quad was required to handle the matrix effects.

A single quad is a relative simple, robust instrument that can handle many applications, and is often used for routine applications. For some applications, e.g. US EPA methods, a single quad is required. A TOF offers either high data acquisition rate or high mass accuracy, which can be useful for some applications and is mandated for certain applications. A trap is useful for mulitiple stages of fragmentation for structural determinations.

A triple quad operated in Q1 mode (single quad) tends to be less sensitive than a single quad as the ion path is longer and ion transmission losses tend to be higher. The higher sensitivity of a triple quad comes from reduction of the noise level, not from a higher signal level.

[yanner]

I will use this instrument for pharmaceutical analysis... if it helps

[gmnydn]

I will use this instrument for pharmaceutical analysis... if it helps

if you will analyse unknowns and try to determine metabolites of pharmecuticals I suggest you that sou should buy a linear iontrap-triple quadrupole hybrid MS/MS. Of course if you have enough budget.

[yanner]

Have you made any positive/negative experiences with Varian GC/MS. I am now very interested in the GC/MS/MS (triple quad) from Varian… so I would be happy to know your opinion. For example why are they much more cheaper than other GC/MS/MS (triple quads). Thank you all for your help .