Discrepancy between Skyline concurrent transitions and Thermo Xcalibur software

Discrepancy between Skyline concurrent transitions and Thermo Xcalibur software Erik  2022-08-25 04:22

Hi Skyline team,

When using the Retention Times - Scheduling graph I always get a totally different picture of how many transitions are concurrent in skyline compared to when I export that transition list to my Thermo method and make the same plot in this software.
For instance with a 4 min window I get max 100 concurrent transitions in skyline but in the Thermo method software I get 350...

Am I missing something or is this normal?


Brendan MacLean responded:  2022-08-25 15:56

Hi Erik,
There was a bug for a few months where Skyline was always reporting the number of concurrent precursors even when the y-axis was labeled as reporting concurrent transitions. Perhaps you have one of the Skyline versions with this bug? Do you have a consistent number of transitions per precursor (e.g. 3 - 6) where you could simply do the multiplication in your head and confirm that the counts differ by that factor?

Hopefully, if you updated to the latest version of Skyline-daily ( or Skyline ( you would see this problem fixed in those versions.

Otherwise, can you please provide screenshots of what you are seeing and upload your Skyline document (use File > Share to produce a .sky.zip file) to the following link?


Thanks for reporting what you are seeing.


Erik responded:  2022-08-26 00:22

Hi Brendan,

Thanks again for your speedy feedback! You were right it was the skyline version! An update resolved the issue.

Thanks for reminding me to keep on updating skyline; if not for new features do it to resolve new bugs ;)!