Shimadzu IT-TOF versus Thermo Orbitrap

[Jinx]

I am looking to buy a LC-MS system for accurate mass determination and structure elucidation of environmental contaminants in soils and sediments. Has anyone have experience with both models? Any suggestion is appreciated.

[jbhines]

Hello Jinx,

I have had quite a bit of experience with both instruments. OrbiTrap is a very nice instrument but when used to perform structural analysis there are some limitations.

First, the optics involved in transfering ions from the LTQ to the Orbi do have some losses associated with them. In testing I found that the LTQ could just about match the depth of MSn as the IT-TOF but this only gives you low mass accuracy. To actually compare you have to acquire with the Orbi and this results in an MSn depth of 1 to 2 levels less than could be achieved with the IT-TOF. For instance, selenomethionine could be fragmented easily to MS5 or 6 on the IT-TOF yet it was only possible to go to MS4 on the Orbi. The only thing I could attribute this to is losses in the transfer optics. The IT-TOF could strip the molecule down to the bare selenium but not on the Orbi.

There is another aspect and this is speed. The IT-TOF acquires spectra about 20 times faster than the Orbi. This means that if you are infusing a fraction for structural determination that you have to sit in front of the machine 20 times longer if everything else is equal. This is not a trivial problem. Sometimes fragmenting out to MS6 or higher you may want to acquire data for 30 minutes to 1 hour on the IT-TOF to get good ion statistics on the lowest intensity (lowest probability) fragments. Multiply this time by 20 and you see the limitation.

If you are going to look at very complex mixtures in MS1 mode then the high resolution of the Orbi is a plus. But most people will perform some sort of separation and collect a fraction for infusion for their structural work. So 100,000 resolution can come in handy if you don't want to have to work at separations but you can get about 25,000 resolution out of the IT-TOF by lowering the signal going into the instrument. This factor of 4 difference means that you can get peak widths of 0.035 daltons on the IT-TOF versus 0.010 daltons on the Orbi. Even though you can see the difference you still can't isolate two ions that close together so you are back to chromatography again on both.

The really nice thing on the IT-TOF is that you can perform really high speed separations with 1 second wide chromatographic peaks and easily collect MSMS and MS3 data automatically. The formula predictor is great too so you can set up automatic methods that will acquire MSn automatically then the formula predictor collects all the MSn data for that parent, calculates losses between the stages and does the data reduction automatically. Also matches isotope ratios as well.

I have not heard a good explanation for it but I am told that the isotope ratios are not faithfully reproduced on the Orbi. In discussions with colleagues I am told that if you lower the resolution of the Orbi then they get better but still not perfect. The IT-TOF doesn't have this problem at all.

So you can see which way I am leaning on the structural elucidation type work. The LTQ is quite a great instrument; fast and rugged. The Orbitrap added high resolution and accurate mass to the LTQ which is a great addition but at a sacrifice of sensitivity and speed. The IT-TOF though is a high speed, rugged ion trap with high resolution and accurate mass for all modes all the time without sacrificing speed or sensitivity.

So if you have other questions just let me know. Both are great instruments but I think for structural elucidation the IT-TOF is more powerful.

[rchapman]

I am in the same position as Jinx. I'm wondering what you think about Waters' Synapt G2 with ion mobility vs. Shimadzu's IT-TOF for metabolite identification, structural elucidation. That would be the primary use of the instrument. However, we would like to include the potential for some metabolomics work and QC control of MAB or fusion proteins.

[jbhines]

I really haven't had any experience yet with the Synapse. We are currently having one installed here at the CCRC so it will be a few months before I get fully into it to see how it runs.

So far though it looks quite nice. A lot of unique features. But I have to wonder how much of an impact the lock-spray will have on very fast LC runs. For instance, I am being told that the lock-spray is set to recalibrate the instrument typically every 30 seconds. But if I am running a fast LC run with 1 second wide chromatographic peaks then the interruption has to be significant.

IT-TOF does not require a lock-spray at all so this is not a problem.

The other concern that I have is sensitivity. For much of our work this will not matter. Some of the modes of operation require very high concentrations so some samples may not work with this instrument. We are lucky in that we have a lot of material to work with so we don't see this as an issue currently.

I am pretty excited though to see the ion mobility data for our compounds. Very nice results from our sample submission!

[Gaetan Glauser]

Hi,

For the Synapt G2,a frequency acquisition of 0.5 sec for the lockspray is recommended. But you can set it at 0.2 s without strong impact on the mass accuracy and this should avoid you to "loose" a peak even though it is 1 s wide.
As for your sensitivity issue, Waters claims a 10e5 dynamic range. I would rather say 10e4.5, which is still pretty good.

[Kostas Petritis]

We have a G2 which we do not use for small molecule structure elucidation so I can not comment really on that (we do mainly proteomics) but it looks like it takes at least 1 sec for the valve to switch between sample and lock-spray and back so even if your acquisition is set for < 1 sec you might still see a 1 sec difference...

1 sec wide peaks in LC... wow!

[Ken]

Not sure if Jinx has make a purchase but, how about considering the new qual quant platform from AB SCIEX, the tripleTOF MS? ^^

Just a suggestions~