Orbitrap or Qtof

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wildcats
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Orbitrap or Qtof

Postby wildcats » Thu Dec 13, 2012 10:11 am

Hi,

We are working proteomics service (ID, PTM) and looking for mass spectrometer.
Then we have two candidates: orbitrap velos pro or bruker maxis 4G.
Do you have any opinion? Estimation (quote) is very similar and our room can modify for maxis.

Thanks

gabe
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Postby gabe » Thu Dec 13, 2012 1:29 pm

I don't have experience working with the Maxis 4G, but my sense is that the Orbitrap is a more-versatile, sensitive, and popular instrument for proteomics. A few things to consider:

# MS^N - ion traps can do higher-order fragmentation (MS3, etc) that can be important for detecting and characterizing certain exotic PTMs. qToFs can only do MS2

# scan speed - I don't know how the newer qToFs compare, but the ones I've used are much slower than ion traps. The MS2 scan speed on the Velos Pro is incredible and I would be surprised if any other instruments can beat it for sheer number of peptide IDs when using CID in the ion trap.

Historically, it was difficult to do isobaric tag quantitation (e.g. TMT or iTRAQ) on Orbitraps due to the 1/3rd rule and poor performance of PQD and ion-trap HCD, but the Velos Pro Orbitrap has a dedicated HCD cell that performs superbly.

honeybadger
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Postby honeybadger » Fri Dec 14, 2012 5:41 am

I have worked with the maXis 4G and a Q-Exactive (not Velos Orbi). In my experience the maXis 4G was VERY sensitive in MS mode, but wasn't always that efficient when we performed tandem experiments. The Velos Orbi will allow you to do complementary ion-ion reactions (CAD/ETD/HCD) which could help improve your PTM discovery and localization confidence. If I was to build a lab up from scratch and was going to peform shotgun proteomics experiments with an emphasis on PTMs, I would go with the Velos Orbi Pro over the maXis 4G... but that's my own opinion

Since you are making a large capital investment, I would send a medium difficulty sample that you expect to get from your clients and have both companies run it on their instruments/data processing suite and see what you get back. We've done that for every instrument that we have purchased and this data really helps us finalize our decision on what platform we will purchase.

Good luck

Christopher
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Postby Christopher » Thu Dec 27, 2012 12:42 pm

I have worked with a very wide array of instruments. I think the choice between an Orbi and a Q-ToF can be difficult these days, there is a lot to consider. In reference to the post a couple up...new generation Q-ToFs are on par, or better than the current gen-orbis when looking at scan speed, when considering that the ToFs are acquiring high-res MS2 data.

I think if I was choosing between an Orbi and a Bruker maxis, I would choose the Orbi for one reason primarily...software support. The selection of software tools available for the orbi is pretty large, and really quite useful. This is especially useful when you are doing service samples. The orbi also gives you a little more flexibility, as mentioned above, for doing PTM analysis (in a bottom up approach...top down is another story). But you can get some cool additional features on Q-ToF instruments these days...such as ion mobility on the Waters Synapts, and the Triple ToF.

I agree with the post above...send a sample, see what they can give you in terms out output.

congriver
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Postby congriver » Fri Feb 08, 2013 10:19 am

Hi,
I agree with the others that the freeware software options are an added bonus for any of the thermo instruments including orbitraps/qexactives. But current generation QTofs are excellent instruments too- they certainly can scan much faster than the orbitrap/qexactive but they also lose sensitivity ie doubling the scan speed halves the signal approximately.... however their resolution remains intact. In orbitrabs increasing scan speed doesn't affect sensitivity as much but it does negatively reduce resolution. I think there are more orbitraps than qtofs used in proteomics primarily because they are so suited to these workflow types which often benefit from a versatile and flexible platform ie CID/HCD/ETD. Either system will do the job-Qtofs work very well in proteomics but orbitraps work even better!


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