Collision Energy on QExactive

Collision Energy on QExactive lisa.j.zimmerman  2013-10-23
Hi Brendan
Has something changed in the way Skyline calculates the collision energy for an inclusion list for the Q Exactive? Previously the values were different depending upon the peptide but now the value is 27 for all peptides?
Also, how is the collision energy calculated for the QEXactive since there is no drop-down option for this….it simply defaults to the Thermo TSQ Vantage?
Brendan MacLean responded:  2013-10-23
Hi Lisa,
This issue, which we fixed for v2.1, hopefully explains what happened:

The QE doesn't use a true CE value, like a QQQ instrument. It uses a normalized-CE, which is usually the same for all m/z values in an inclusion list. They apply their own regression to these values. The original behavior was a mistake in the understanding of nCE on a QE instrument.

Isolation (or inclusion) lists exported for QE now simply ignore your CE equation setting, no matter what you have selected.

Hope that helps to clarify.

Tobi responded:  2019-04-29
Dear all,

to quickly pick this up, the QE HF seems to allow also the use of absolute CE. Does that mean CE optimization would be possible if one would be creating the inclusion lists by hand in excel? Or does it make the most sense just to go with one NCE for all peptides and let the thermo software handle the rest?

Brendan MacLean responded:  2019-05-01
Hi Tobi,
Thus far, we have not seen enough interest in optimizing absolute CE on the QE. Our own lab uses a single NCE. If someone produces research that shows they can do better in an important way than the NCE values by optimizing with absolute CE, we would certainly consider adapting. You could derive the absolute precursor CE values simply by asking Skyline to export a Transition List and then using the per precursor CE values Skyline outputs in your isolation list.

If you find anything we should know about, please let us know. Otherwise, this should at least work as a hack workaround.