Number of data points per LC peak vs cycle time in scheduled MRM

Number of data points per LC peak vs cycle time in scheduled MRM benoit fatou  2018-10-15

Hi Brendan,
I am currently using a QTRAP 5500 for scheduled MRM experiments on tryptic peptides.
I was wondering if the number of data points per LC peak (see attached file) is correlated with the cycle time settled in the instrument method.
Thanks for your help,

Brendan MacLean responded:  2018-10-15

Hi Benoit,
Yes, the two should be related. The width of your peak, divided by the instrument cycle time at the time it was collected should give you the number of points across your peak. If the method is scheduled then cycle-time may not be a value you can set in the method. You might set only the transition dwell time instead and cycle time could vary depending on how many transitions are being measured concurrently at a given time. Which can even mean that the intervals between the measurements in your peak are not consistently spaced.

Hope this helps. Thanks for posting to the Skyline support board.


benoit fatou responded:  2018-10-15

Hi Brendan,
Thanks for your quick response.
In the ABSciex instrument method, I can set the "Target Scan Time" in a scheduled MRM mode.
Is this term related to the cycle time or the transition dwell time? Because for me, it seems to be related to the cycle time.


Brendan MacLean responded:  2018-10-15

Sounds like you know your instrument:

"Target Scan Time (sec) field. The total scan time is adjustable so that a specific number of points across the LC peaks can be targeted."

benoit fatou responded:  2018-10-16

Hi Brendan,
You are right about the instrument but I am still confused because we set this time in the method but he could change according to the number of transitions pairs to monitor. To know exactly the time spent for each transition in a scheduled MRM mode, we need to calculate in a specific time because we will have different number of transitions at this time.

Is the "Retention Times - Scheduling" graphic representation provided by Skyline able to give this kind of information?

Thank you very much for your help.


Brendan MacLean responded:  2018-10-16

I hope the scheduling graph is useful, but you probably need to do your own research on how the instrument responds to different settings. I hope that both the scheduling graph and the points across the peak chromatogram graph detail will give you new insights. If you have any, please post them here.

I guess I expect an instrument with a target cycle time to need to vary dwell time based on the number of transitions to monitor at any given time, since essentially the relationship is (ignoring switching time between transitions):

transition count * dell time = cycle time

To keep cycle time constant through changes in transition count, then dwell time would have to change.

Dwell time is likely the least visible value in this equation.

  • Transition count over time is shown in the scheduling graph
  • Cycle time can be understood from the points across the peak information (and Target Scan Time on the method)

As far as I know, dwell time is not recorded in the data. But that is an interesting idea to have Skyline graph it in the RT scheduling graph. It could do this a priori if you gave it the "Target Scan Time" or we could also graph dwell time from raw data by counting the number of transitions measured in a period of time.

But, unfortunately, we don't yet do either. You could probably pretty easily invert the scheduling graph in Excel, by using right-click > Copy Data, pasting the graph points into Excel and then adding an equation column "=TargetScanTime/TransitionCount" where TransitionCount is the value from Copy Data.

Hope this helps. Good luck with working out your optimal settings.