I recently had the opportunity to analyze the same (intact protein) sample on an Agilent QTOF and a Thermo Q-Exactive, and noticed that in addition to having a moderately higher resolution the orbitrap appeared to generate much "cleaner" deconvoluted data, as in many apparent adduct/variant/glycoform peaks that were present in the QTOF data were completely absent for the orbitrap data.

What is the source of this difference? Could the orbitrap be simply not detecting these other species or the QTOF generating these other species as artifacts?

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    $\begingroup$ I’m no expert in MS, but is this an unexpected result? They’re different kinds of instrumentation, and much of the product literature for Orbitrap systems focuses on cleaner baselines and better resolutions for intact proteins $\endgroup$
    – NotEvans.
    Dec 31, 2021 at 10:18
  • $\begingroup$ (Only user-perspective about MS, rather than method development:) higher resolution reads like different a priori design features and parameter settings of the MS experiment yield results of better quality (like low resolution bench-top vs. sector field or tandem MS-MS high-res MS, or using MSes by different vendors). Deconvolution, on the other hand, is about intelligent signal processing of already recorded raw data. So, there may be a blend of reasons. $\endgroup$
    – Buttonwood
    Dec 31, 2021 at 10:42
  • $\begingroup$ @NotEvans It's not without tradeoffs though. I know that higher resolution comes at the cost of slower scanning speed, but could cleaner baseline also be coming at the cost of non-detection of lower abundance species? $\endgroup$
    – oryza
    Dec 31, 2021 at 22:44
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    $\begingroup$ Deconvolution is very noise sensitive and we have no clue how the black-boxes software enchance resolution. They will never tell. $\endgroup$
    – AChem
    Dec 31, 2021 at 23:10
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    $\begingroup$ You might get decent response if you add more details about deconvolution. What deconvolution method are you using? What is meant by cleaner? Does it mean higher signal-to-noise ratio? $\endgroup$
    – AChem
    Jan 3, 2022 at 1:16

1 Answer 1


Lots of differences between TOF instruments and Orbis. Orbitraps are Fourier Transform mass analyzers, so the longer you let the Orbi "scan" a packet of ions, the cleaner the signal becomes (signal averages towards the positive, noise averages towards zero). That's where the FT deconvolution comes in.

The drawback to the Orbitrap is with duty cycle. While the Orbi is "filled" and measuring those ions, there's still a beam of ions coming from the source. They either get utilized by another mass analyzer/component (i.e. an HCD cell for MS/MS fragmentation in parallel to the Orbitrap acquiring the MS1), or get thrown out entirely. If you're measuring a complex sample and using liquid chromatography before the MS, that means you're losing out on analyzing an ever-changing beam of ions.

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    $\begingroup$ Welcome to SE Chemistry, but I apologize because there are a couple of conceptual problems in the answer above. Noise does not average to zero in time average...this is a persistent myth. David Traficante has addressed this beautifully in his myth-buster article "Time averaging. Does the noise really average toward zero?" doi.org/10.1002/cmr.1820030203 $\endgroup$
    – AChem
    May 11, 2022 at 1:58
  • $\begingroup$ Secondly, Fourier deconvolution is wildly noisy. It goes haywire with a small amount of noise even in a clean synthetic signal... thus they would not be using Fourier deconvolution methods and produce a better "deconvolved" spectrum even after applying window functions. Mostly likely they are using more sophisticated deconvolutions such as maximum entropy deconvolution, which is far better than Fourier deconvolution. $\endgroup$
    – AChem
    May 11, 2022 at 2:01
  • $\begingroup$ The OP never bothered to follow up and explain more. I wish he had added more information about his data. $\endgroup$
    – AChem
    May 11, 2022 at 2:02

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