Skyline failure_metabolomics_methods containing high number of transitions anna illiano  2021-06-18

Good afternoon.
I have a couple of problems in using Skyline for metabolomics.

  1. The software does not allow me to simultaneously monitor all the transitions present in the method (more than 400). I need to create multiple methods to analyze a single sample.
    When I try to upload a sample by inserting all the target molecules in the skyline, I get this error message:
    "Failed importing results file
    An item with the same key has already been added. "
  2. Even if I prepare methods containing fewer transitions, for some molecules Skyline does not allow me to evaluate the TICs even if by using the Analyst Software (Sciex) I am able to see and integrate that transitions and TICs.

Can you help me?


Brian Pratt responded:  2021-06-18

Hi Anna,

I'm sure we can get this working for you.

Can you please provide:

  • Your current Skyline document (use Skyline's File > Share menu item to create a file)
  • The transition list you're wanting to import into Skyline
  • The raw mas spec data you're wanting to analyze in Skyline

You can upload to , or if you prefer something private we can use whatever method is convenient for you.

Thanks for using the Skyline support board!

Brian Pratt

Brian Pratt responded:  2021-06-18

(I should mention that 400 is actually a very small number of transitions by Skyline standards, by several orders of magnitude, so don't be concerned about that.)

anna illiano responded:  2021-06-21

Good morning Brian Pratt,

may I have an email address to send you the files that you need?


Anna Illiano

Brian Pratt responded:  2021-06-21

Certainly. I will contact you privately.


Brian Pratt responded:  2021-06-22

Hi Anna,

Thanks for providing your files. I am happy to report that there's a simple solution to your problem.

The Skyline Targets tree has a hierarchy Molecule List > Molecule > Precursor. The way you have imported your transition list, the column of molecule names is being interpreted as a column of Molecule List names, so you have many molecule lists, each with a single molecule, whose names are created by Skyline based on the Q1/Q3 values. But these Q1/Q3 pairs are not unique across your transition list, and the result is that some molecules appear in more than one molecule list, which Skyline wasn't expecting.

If you simply declare that column of names to be the "Precursor Name" column at import time, you will have a single (automatically named) Molecule List, and a few hundred distinctly named molecules below that, each with appropriate transitions below that, and everything will work smoothly from there.

We will work on improving this error message, thanks for helping us improve Skyline!


Brian Pratt