Both are good systems. The Q Exactive has a higher resolving power but a slower acquisition. With a Orbitrap analyzer a higher scan speed implies a lower RP (the specs are given for m/z 200 but not as good for higher m/z...). The Waters Synapt has indeed the additional IMS separation capability. If you have experience in one of the other software package this may be also something to consider. The best thing is to try them with your samples.

One of my friends just got his Q Exactive just two weeks ago (he also has a Orbitrap Xl as well as a Velos). In a direct comparison of a HeLa cell lysate (in solution digest) splitted in half he could identify about 600 proteins on the Velos, but about 2200 proteins on the Q Exactive (both with HCD fragmenataton; short gradient of about 60min, Proxeon Easy nLC, Proxeon ESI source, 15 cm column, 75µm ID, 3µm C18 from Dr. Maisch, MaxQuant 1.2.2.5). So the Q Exactive seems to be VERY, VERY good for complex samples and proteomics applications. A disadavntage of the Q Exactive however appears to be cleaning, which is required every 6-8 weeks also depending on your samples and involves quite a bit of screwing. It is not just cleaning of the S-lens but also of the quadrupol etc. Translates into about 1 day of down time. I don´t have any experience with Waters mass specs.

Both have pros and cons. We are testing quantification on the Q Exactive compared to triple quad based systems. Q exactive is performing quite well. We have already Waters Synapt (G1/G2), and Ultraflex TOF-TOF for discovery and look for a validation instrument.

WATERS Synapt G2 is better due to its UPLC seperation system which is very good for proteomics analysis.

Thanks for the valuable input we definitely deal with mostly complex samples, human and animal for clinical proteomics etc. Although it will ultimately come down to price as well. Thermo is putting in much more effort to work with us on price and making it fit our budget. I will have to weight the costs. I wasn't aware that the Q Exactive would need cleaning so frequently. We already have an old QSTAR and the downtime on that is very bad which is why we need to get rid of it. I was told that Q Exactive identifies more proteins by Thermo and that was because of the higher scan rate than any other instrument but it depends on the resolution you're intersted in for protein ID and the specific application. The faster scan rate the better the sampling of the UPLC and greater protein ID's. Last months issue of Mol. Cell Proteomics was all dedicated to instrumentaion development and the focus on Progress of the European 7th framework project for the PROSPECTS project. This was a multi-institutional collaborative 5 year project coordinated by Matthias Mann for development of instrumentation and applications to biomedicine. The articles in reported on the the development characterization, application and comparison of the Orbi Elite, Velos and Q Exactive in high througput proteomics ID. From the read seems like the Q Exactive may be a better option. Although the Thermo rep did mention that the Waters has the Ion mobility and computation analysis for MS[e] fragmentation much more developed hand their software and that the Waters Ion mobility integration is much more developed as well since Thermo employs ion mobility at the source instead doing a quantitative separation within the instrument using TriWave separation. Our institution is more open for a 24 month lease for two years at this point because tehnology changs so fast with improved electronics and configuation the would rather exchange it for an updated model until they decide to buy. The monthly cost difference per month may be as much as $10k! But we need one that versatile to do complex proteins, DXMS and more ID's which I think the the ion mobility , MS[e] and greater sensitivty are key components of this. Any further experience from anyone is greatly appreciated as well. Waters also boasts that the Synapt G2-S usually goes mantenance free for a year with no problems.

I personally would always go with Thermo. Period. Hope this helps, brief as it is. I admittedly don't know much about the Waters instrument. The QExactive is a terrific instrument, and I trust Thermo to deliver an instrument that works.

I have worked with Synapt G2 where the IMS is breakthrough tech for the Proteomics and especially for the PTM and SILAC, it would be the better choice compare to Q exactive

No but that's true I can't make any comparison until I try them or have samples run on them. Although I don't think the peole that have used the Q Exactive have actually tried the Synapt either to make a true comparison. From the technical standpoint and the functionality seems like the Synapt would be much more versatile and Waters has the software won and already to go for analysis of Ms[e] data and ion mobility in a quantitative manner. ABSciex and Thermo I believe have ion mobility enabled just for ion selection ad not for quantitative applications. I did test the improvement of protein ID's using Ion mobility versus not and I got two fold more ID's with IM than without. Although I'll have to check to see how the protein IDs compare to the orbi. I think they were just as comparable but more using IM.

The accurate comparison of different MS is always difficult. Because from the sample preparation to the filter of results, all these steps will affect the IDs. However, one point is very clear. Higher resolution of parent and fragment ions, more confident peptide and protein identifications. For Q-Exactive, MS1 70 000, and MS2 35 000 (m/z 200) is the typical setup. The mass error of MS1, usually less than 5 ppm, and MS2 less than 20 ppm. This will very very helpful for confident identifications. Except this, from my experience, usually top 12 method on Q-exactive, the cycle time is around 2 s depend on parameters setup, which is very good for UPLC separation. For the identifications, more than 1000 protein groups and 5000 peptides can be identified easily with single 1-2h run.

We do have a Synapt G2-S in our lab - and after optimization of UPLC and MS methods can also get around 1500-2000 IDs from e.g. mouse cell lysates in a 2 h run. Quite on par with Q-Exactive.

Mass accuracy on the G2-S is < 2 ppm for most peptides in resolution mode, and if you run high-resolution mode, even

We do have both in the lab but the QExactive just arrived and is not yet installed. We made our choice for the Qexactive for its dual capacity, both in discovery and in quantification. It appears as sensitive as the new generation of triple quadrupoles. More news soon.

Your feelings are right!

We acquired Synapt G2 recently (2012) and are very much satisfied with the maschine.

First, it is very user friendly to operate, calibration and maintenance of the the system is quite simple.

Second, Waters provides essential support and consultations (at least in our country--Lithuania).

Third, as we all most interested in quantitative proteomics, this machine is excellent: no need to use chemical labels and isotopes.

PS: Please, do not relate my comments with corporate advertisement.

Dear Dennis

In our experience, if it is difficult to choose between two such expensive instruments, you must go for the one in which you will get the the best after sales service from the company in your region. An experienced MS technician is worth his/her weight in gold and the company support is essential!

Regards

Marina

PS. By, way, I am a Synapt fan and we get excellent results on UPLC-MS, MS and MS-MS, even on larger proteins (

I've been using the Synapt platform for our quantitative shotgun proteomics experiments, and it has provided good results so far. We recently aquired a Q-exactive, and our mass spec researchers are very enthusiastic about its potentials. My feeling is, for quantitative shotgun proteomics, MS[e] is, in theory, a more "correct" approach, in that the full ion intensity reaches the detector (so it's fairly lossless), while, in practice, Thermo's Q-exactive has consistently provided better results, even for label-free quantitative proteomics. And, most importantly, either equipment will produce results that demand confirmatory work. Our quantitation CVs for the Synapt are quite high, because of the difficulties in consistently achieving a "top 3" identification when working with alternating low/high collision energies, which ultimately lead to sub-optimal parent ion fragmentation. I love the theory behind MS[e], but I agree that the Q-exactive will allow better results with a label approach (using iTraq, dimethyl, or SILAC), and better PTM analysis, so you should keep that in mind as well.

Hi everyone, really exited when googled this topic although it's been posted for 3 yrs. Recently our core is planning to acquire a high-def. MS for applications in biologics analysis (esp. biosimilars, mAbs) with minor proteomics/biomarker research. And we found ourselves exactly in the same situation: Waters Synapt G2 S, or Thermo Q-Extractive? However our focus is quite different from Dennis's (biopharma vs. proteomics). So, does the versatality Synapt offers valued more than the superior resolving power offered by QE? Any comments or suggestion is appreaciated!

At this point there are more offerings, Agilent now has an IMS QTOF with roughly double the resolution of the Synapt and Waters has a new IMS platform in addition to the aging G2S.  I've not seen the performance of these for your particular application, but depending on the m/z range resolution could be similar between the TOFs and QE.  In the proteomics work I've done at Bruker, running fast ms/ms cycles we saw that above m/z 900 even our lower resolution TOFs have higher resolution than the QE.  Unfortunately we don't have a an IMS instrument on the market yet (I've worked on the project for three years) but are working to release one in the near future.  There are many options out there and any instrument vendor should be more than happy to give you a demo and show exactly what they can do for your application.   

Thank you Mark, very helpful. Now we are inquiring Waters for their newer Synapt G2-Si and Vion models. And for higher m/z, Thermo recommended their Exactive Plus EMR (Extended Mass Range) model, yet it seems this one do not have the Q option

I would like to suggest that you not only look at the capabilities of the instruments but also the capabilities and ease of use for your application of the software supplied by the two companies.  It is just as important to be able to process the data as acquire it.

One thing one should consider in a demo run is the detector fatigue phenomenon. Basically, one would want to see constant intensities over a short period of time, says if the instrument is running continuously for 24 h. 

If you want to do untargeted metabolomics, Q Exactive is the best choice: great mass accuracy, robust sensitivity, and the bioinformatics part is both powerful and easy to use.