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?

Greetings,
Erik
 
 
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 (22.1.9.208) or Skyline (21.2.0.568) 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?

https://skyline.ms/files.url

Thanks for reporting what you are seeing.

--Brendan
 
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 ;)!

Greetings,
Erik