Wrong idotp in small molecule mode

Wrong idotp in small molecule mode Noortje  2023-05-03 06:07

Dear Skyline support,

I noticed two small bugs in the small molecule interface. One of them I found back in a post from Chris Ashwood in 2019: https://skyline.ms/announcements/home/support/thread.view?entityId=712b51a4-fe69-1037-86c0-e465a393641d&_docid=thread%3A712b51a4-fe69-1037-86c0-e465a393641d

I have the same problem: when I open a new Skyline file, and load my small molecule data, the initially calculated IDOTPs are very low and not correct. Saving, closing and restarting the file solves the problem. This is an easy workaround, but confusing for people that are not familiar with the problem.

The other thing I encountered is also in the small molecule interface:
My settings are: Transition Settings>Full scan>MS1 filtering>Isotope peaks included, count 3 (also happens when using percentage)
When I then load the transition list, still only 1 isotope is included.
The problem is solved by changing the isotope settings to something else and back.

Thank you and best wishes,

Brian Pratt responded:  2023-05-03 09:16

Hi Noortje,

Thanks for reporting these problems.

The Peak Count issue has been fixed for the next Skyline release.

We have not managed to reproduce the idotp issue, can you provide the files and describe the settings and steps necessary to demonstrate the problem?

Thanks for using the Skyline support board!

Brian Pratt

Noortje responded:  2023-05-03 23:55

Hi Brian,
Thanks a lot for your response.

I find it hard to pinpoint exactly what causes the idotp problem, but I can reproduce it e.g. when:

  • Open a new file in Small molecule mode
  • Start from default settings
  • Adjust the Transition Settings to the ones in the attached .sky file
  • Load the attached transition list
  • Load the attached data file

See print screens of the problem in the attached pptx. After saving, closing and reopening, the idotp is correctly calculated (see print screen)

I hope this is clear! Thanks,

Shared files: