benchtop mass spec - which would you choose between -Qexactive or velos pro

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congriver
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benchtop mass spec - which would you choose between -Qexactive or velos pro

Postby congriver » Thu Mar 14, 2013 7:39 am

Hi :)
I have the option to pick a general purpose machine to choose from above) to support a proteomics lab which would you choose as the best all round system to support protein id, PTM and quantitation. Maybe you could state your reasons for protein id, PTM and quantitation by isotopic labeling stratagies. I havn't used either system. I suspect the Qexactive may be better for quantitation but not so sure about the other workflows.
Thanks
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Postby Infinity » Thu Mar 14, 2013 9:50 am

For me the choice is obvious - QExactive. We have both QExactive and LTQ Orbitrap Elite and QExactive gives ~ 2 times more ids for complex samples.

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Postby gabe » Thu Mar 14, 2013 9:56 am

You can't do SILAC (or other MS1-based quantitation techniques that require high-res mass) on the Velos Pro. The QExactive is definitely more-versatile, but I'd be a little nervous about going with such a new instrument design, personally.

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Postby Christopher » Fri Mar 15, 2013 5:09 am

Assuming you mean the Velos pro ion trap, and not the Velos pro orbitrap, then it really is a no-brainer, the qExactive. The qExactive is a nice system for IDs, quant, and some PTM applications...you can even do some nice (albeit, mass limited) top down workflows with it. There are certain areas where a system setup like the elite or a conventional LTQ orbi would be better suited, but as an all around system, the qExactive is quite nice.

One thing to keep in mind is that the qExactive is more work to maintain than the Velos Pro. You have to be pretty diligent with the cleaning and calibration, but this is not such a big deal. I would still choose the qExactive.

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Postby gadsouza » Wed Mar 27, 2013 2:03 am

gabe wrote:The QExactive is definitely more-versatile, but I'd be a little nervous about going with such a new instrument design, personally.


the QE is available for almost 2 years now if I am not mistaken, which is a lot of time considering the 1st Thermo Orbi is not even 8 years old. So I guess is pretty easy to find an owner that can give you some decent input already.

I can tell you, for example, that if you are running heavy-duty proteomic samples (i.e. very complex samples in long gradients etc), you are going to need cleaning on your quadrupole very often. And by that I mean once every 4-5 weeks.

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Postby Doug » Wed Mar 27, 2013 9:43 am

I have heard great things about the Q-exactive but I have also heard a lot about very frequent maintenance/cleaning. Can you elaborate on that a little? What is required? Venting and wiping parts with methanol? What parts require cleaning? Just the rods or parts of the source as well? And is this something the user can perform without s service call? Or does is require a visit from a service rep in order to maintain the warranty? And what is the average downtime for this maintenance? Just one day (cleaning and overnight bake out)?

I have heard some vague information regarding this maintenance but I think knowing more specifics would really help out the community in making decisions between the Velos Pro and the Q-exactive.
"If we knew what we were doing it wouldn't be research." -AE

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Postby Christopher » Mon Apr 01, 2013 9:20 am

Doug, as far as the cleaning and maintenance goes I can provide some insight. The cleaning requires venting, taking the quad and s-lens out, and cleaning with your method of choice. This is something you can do on your own, but I would recommend the appropriate training from Thermo. What, if any, affect this has on your service contract or warranty, I do not know. The average downtime is about a day. It takes about half the day to get the parts out, clean them, and reassemble, then bake it out overnight. Then another hour or two to get it calibrated and tuned up to run again (this can vary depending on the status of the instrument prior to cleaning).

From what I understand Thermo have made some changes in the latest instrument control software that help keep the instrument clean. I have only heard rumors about what was changed, as I guess there was a pretty critical error, so I don't really want to speculate here about which is true.

Personally, I think that if treated properly, the qExactive can be as robust as a Velos Pro for stability of calibration and sensitivity across a large number of injections. In my hands, this is certainly the case. I don't really agree with the comment from gadsouza above. I personally run very complex proteomic samples down a 45cm column interfaced to a qExactive almost 24/7. I do not see the need to clean the quad every 4 to 5 weeks, it just isn't necessary.

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Postby gadsouza » Mon Apr 01, 2013 11:30 pm

Indeed apparently new Tune version will reduce but not eliminate the need for cleaning, but I do not know any details as well.

Christopher I would say you are probably lucky then, not only me but other QE owners I happen to discuss things from time to time observed similar trend.

But regardless of personal experiences the quad cleaning is very easy to track through the Tune (the quad Endurance test) or checking ms/ms % identification in a test sample.

I would still get a QE over a Velos Pro without a thought.

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Postby Christopher » Tue Apr 02, 2013 3:22 am

Yes I agree, it is quite easy to track and you definitely know when your quad is dirty as the performance drops quite a bit. I have also heard similar things from other QE owners, but I always felt they were exaggerating, hopefully my good luck continues!

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Postby daniswan » Wed Apr 03, 2013 6:38 pm

With regards to the cleaning process: as someone with considerable experience/comfort level in taking apart instruments I will say that cleaning the quadrupole in a Q-exactive is not a trivial task. The problem is that you have to vent and take apart the system from both the front inlet and from the back (orbitrap/ctrap side) to get the quadrupole out. So by the time you get the quad out you will have a pile of screws and removed parts on the bench. I would classify it as "major" rather than "minor" surgery. Our system is still under service contract, so I have not done it myself, but I have seen the process several times. The service engineer comes out every ~6-8 weeks and cleans ~10 parts with methanol and/or more recently with aluminum oxide. It takes him around 3-4hrs one day, and then about another hour the next day for calibration. The best diagnostic measure we have found to identify when our system is dirty is peptide identifications on a complex standard (yeast WCL). A dirty quadrupole MS1 signal is not that different from a clean quadrupole. However, peptide identifications on a dirty system can drop by ~70%.

With regards to performance: We have both a Velos orbitrap (not a pro) and a Q-exactive. When the Q-exactive is nice and clean it always out performs the Velos in peptide and protein identification numbers by a substantial margin. I would say the primary reason I use the Velos for some samples is when I have samples with large dynamic range and reduced complexity. Here the ion trap sensitivity on the Velos allows me to identify the lower abundance peptides in my sample better than the Q-exactive.

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Postby bphinney » Thu Jun 27, 2013 8:39 am

We have two QE's and indeed the quads need to be cleaned every 6-8 weeks if you run very complex samples. Apparently it's the isolation step that causes it to be dirty, so the more MS/MS you do (e.g. more you isolate) the dirtier the quads become. Of my QE's One is still under contract but the other is not and thermo wants 6-7K each time they clean it. That's crazy as that would cost over 40K a year. Word is they also will not cover more than 2 or so cleanings even if you have a service contract.

From looking at the diagrams of the new fusion it appears to me that it will have the same issues as the QE so I would be pretty cautious about that one as well. When the QE's are not dirty they are beautiful instruments. Just be prepared to spend an extra 40K a year if you want thermo to clean your quads routinely.

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Q-exactive

Postby karthikskamath » Wed Jul 31, 2013 8:22 pm

http://planetorbitrap.com/data/uploads/51f0547a7fd5a.pdf

This documents shows much improvements at least in software part of Q-exactive based work. My favorite is introduction of centroid mode of data acquisition. This will help to reduce the data size by 3 times. There is also a automatic check for Quad cleanliness status!! Did some one start using this already?

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Postby bphinney » Thu Aug 01, 2013 8:26 am

karthikskamath wrote:http://planetorbitrap.com/data/uploads/51f0547a7fd5a.pdf

This documents shows much improvements at least in software part of Q-exactive based work. My favorite is introduction of centroid mode of data acquisition. This will help to reduce the data size by 3 times. There is also a automatic check for Quad cleanliness status!! Did some one start using this already?


yeah, I guess before we were using non-intelligent beam management lol. I don't think that quad isolation cleanliness test is new. It still takes 15 minutes and requires the infusion of cal mix. Unless there is a new test I haven't found yet. Centroid mode is nice however. Should save me some money on hard drives. Although I haven't switched over to it yet. I got used to profile and I'm afraid I'd miss it.

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Postby Leadazide » Thu Aug 01, 2013 8:34 am

Many of my customers (if not all) have been migrated over to the 2.2 SP1.. And with great succes.. if the advice regarding lower target values is followed.. Otherwise there is no benifit.

The Quad test is not new to 2.2 SP1 but the intelligent beam management is.. that and the DIA. Combined it should be more than enough reason to upgrade.

A lot of new diagnostics have also been added to the 2.2 SP1 but these are only available for service engineers so there is no direct benifit for the customer but for troubleshooting and diagnostics they are must-haves. This is the main reason I have been pushing the 2.2 SP1 for my customers.

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Postby bphinney » Thu Aug 01, 2013 9:06 am

Leadazide wrote:Many of my customers (if not all) have been migrated over to the 2.2 SP1.. And with great succes.. if the advice regarding lower target values is followed.. Otherwise there is no benifit.


I'm skeptical, if you are running a very complex sample with a lot of material than you will be constantly acquiring MS/MS anyway so I don't see how lowering the MS/MS AGC targets or decreasing the max trap time will = less time isolating during the LC-MS/MS run. if you're sample is not very complex, then yes I can see how that would make a difference. What am I missing?

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Postby Leadazide » Fri Aug 02, 2013 2:17 am

bphinney wrote:I'm skeptical, if you are running a very complex sample with a lot of material than you will be constantly acquiring MS/MS anyway so I don't see how lowering the MS/MS AGC targets or decreasing the max trap time will = less time isolating during the LC-MS/MS run. if you're sample is not very complex, then yes I can see how that would make a difference. What am I missing?


If you go to Planet Orbitrap and download the "Achieving Peak Performance with Q Exactive Instrument Software 2.2 SP1" and read the part about Intelligent Beam Management it should explain.. I found the two slides on page 24 and 25 the best for visually explaining the differences and why it is a benefit..

Hope this helps.


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