Dashed red lines/number

Dashed red lines/number Michael Cundell  2018-11-21

Super basic GUI question.

I have heavy/light labels. When I select a transition for either label, what do the small vertical dashed red lines that span the x-axis and the corresponding red number refer to in the chromatogram view?

At first I thought that these corresponded to the number of datapoints for which the transition is observed across the peak. However, I have light labels with nearly no signal yet a lot of the red dashed lines. Then I thought ok its just the number of datapoints in the heavy label. However, the number between the heavy and light label is often slightly different for the same transition. I cant seem to rationalise what they mean.



Brendan MacLean responded:  2018-11-21

Hi Michael,
It is the number of measurements of the transition made by the mass spectrometer between and inclusive of the integration boundaries. A very simple concept in SRM, as mass spectrometer cycles through each transition and gives it a certain dwell time regardless of what hits the detector. In full-scan chromatogram extraction, it becomes the number of spectra from which we attempted to extract a chromatogram point based on the transition to spectrum matching rules. In PRM, that is the number of spectra with a matching precursor m/z, again regardless of whether the spectrum contains any signal, because the precursor m/z values match the spectrum is considered to contain a valid measurement of the transition. Hopefully, you can work out the corresponding transition - spectrum matching rules for MS1 and DIA fragments.

So, again nothing to do with signal. It is the number of valid measurements of the transition made by the mass spectrometer, based on the matching rules defined by your transition settings.

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


Michael Cundell responded:  2018-11-21

Hi Brendan,

All is clear now... thank you for clarifying!!