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Assistance with Importing Transition Lists into Skyline for Molecule Interface

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Assistance with Importing Transition Lists into Skyline for Molecule Interface anirudhkashyap511  2025-01-08 09:37
 

Hi Skyline Team,

I have written a script to automate the import of transition list CSV files into Skyline. My code is structured as follows; it is looping across all csv files.

%SKYLINE_CMD% --in=%INPUT_SKY_FILE% --import-transition-list=!TRANSITION_LIST! --save --out=!OUTPUT_FILE!

Here:

INPUT_SKY_FILE is my template Skyline file, saved in the molecule interface.
Each TRANSITION_LIST file contains the following headers:

Molecule Name Precursor Mz Fragment Ion Precursor Charge Collision Energy Product Mz Product Charge Explicit Retention Time Explicit Retention Time Window

This script worked correctly when I used the peptide interface and had PeptideModifiedSequence in the headers. However, now that I am working with the molecule interface and using Molecule Name, the transition list fails to import properly.

Could you please provide guidance on how to modify the script or troubleshoot this issue? Are there any specific changes required for importing transition lists into the molecule interface?

Thank you for your assistance.

Best regards,
Anirudh
 
 
Brian Pratt responded:  2025-01-08 11:19

HI Anirudh,

Can we have a look at an example transition list CSV file?

Thanks for using the Skyline support board,

Brian Pratt
 
anirudhkashyap511 responded:  2025-01-08 13:03

When i copy paste it it works fine, But when I try to use the command line. It still expects a peptide for some reason.
 
Brian Pratt responded:  2025-01-08 13:49

That does sound like a bug - could I also see an example of the Skyline document you're using? There must be some kind of interaction there, as this is a scenario that we do normally support.

Thanks,

Brian
 
anirudhkashyap511 responded:  2025-01-08 14:24

Hi Brian, thank you for your response. This is the template skyline file I was using to copy.
 
Brian Pratt responded:  2025-01-08 16:20

OK, try changing "Fragment Ion" to "Product Name" and it should work fine. Skyline didn't recognize that column name. When you paste the CSV into the Skyline UI, that comes up as "ignore column", so it doesn't actually work there either but Skyline is less mysterious about it.

So, the bug here is that SkylineCmd is doing a poor job of explaining itself, giving a very misleading error message. I'll put that into our development queue.

Thanks for letting us know!

Brian
 
anirudhkashyap511 responded:  2025-01-09 07:01

Thank you so much Brian, worked! Thats an interesting bug haha.