Issue 435: Problem handling 'Optimize CE' data

Assigned To:Guest
Opened:2015-10-11 by stolltho
Changed:2016-01-06 by Brendan MacLean
Resolved:2015-10-16 by Brendan MacLean
Duplicate: 51
Closed:2016-01-06 by Brendan MacLean
2015-10-11 stolltho
Title»Problem handling 'Optimize CE' data
Assigned To»Brendan MacLean
Skyline vers
mass spec Agilent 6490 QQQ

Hi Brendan
Tried to use Skyline to optimize CEs. Had couple of issues, esp. #3 confused me a lot:
1. Imported data for second half of the precursor not displayed (see page 1 of ppt, red square)
2. Had +/-6 CE steps, step 6 never shows up in imported data (see page 1 of ppt, blue squares)
3!. Analysing 'Opt CE' data in skyline vs Mass Hunter Qual result in different optimal CE values. It seems in skyline there is always a shift of the CE steps in the peak area histograms: Step -1 is actually step 0!!! Don't know how to explain this in a better way. Refer to page 2 of ppt.
4. It would be nice if skyline could not only show the step# but also the CE, eg. Step -6 (9V)

There is something weird going on.


2015-10-16 Brendan MacLean
resolve as Duplicate of 51
Hi Thomas,
In order to go to 6 steps, you will need to expand the "Method match tolerance m/z" in the Transition Settings - Instrument tab. I think 0.065 should work. This is a duplicate of the long-standing issue 51. It happens because Skyline introduces a slight shift in precursor m/z for each CE step, and when that shift is great enough it will move the chromatogram precursor m/z outside the range that Skyline will accept as matching the target.

Thankfully, still very few people have tried to expand the number of steps beyond 5, probably because of the impact on the number of transitions that can be measured. More often we have seen people decreasing the step count (e.g. to 3) and increasing the step size. I believe this is what Agilent recommends.

Hope this helps. I agree on showing the voltage and wish that we could in all cases record the actual voltage used by the instrument. If we could do that reliably, then we wouldn't need the m/z shift. Unfortunately, not all instruments report the true CE voltage used for each transition, which makes it difficult to confidently declare anything other than that a chromatogram matches a certain "step", and even then, as you have seen, the matching is somewhat delicate. Wish we could do better of course.


2016-01-06 Brendan MacLean
Assigned ToBrendan MacLean»Guest