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Issue with Skyline v25.1.0.142 Handling MS1 Data from DDA Files

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Issue with Skyline v25.1.0.142 Handling MS1 Data from DDA Files Luisa Nieto Ramirez  2025-08-21 09:28
 

Hello

I’ve been experiencing a consistent issue while trying to build a PRM method from DDA data using the latest Skyline version: 25.1.0.142 (7401c644b4). The chromatograms for my precursors are either completely empty or display an abnormal trace. Out of 13 synthetic peptides, only one might appear in a single sample, and inconsistently at that.

To troubleshoot, I tested older DDA datasets that previously worked well. Unfortunately, the same issue occurred in version 25. However, when I switched to another computer running Skyline v24.1.0.414 (5b5ea5889c), I was able to see all chromatographic peaks correctly, both for the older and newer DDA data.

It appears that version 25.1.0.142 is not properly handling MS1 data extraction from DDA files. I’m not sure what the underlying cause is, but this behavior seems specific to the latest version.
 
 
Nick Shulman responded:  2025-08-21 10:09
Can you send us your Skyline document and one or more of your raw files?

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

The "Share Document" dialog gives you the options of including the raw files in the .zip file or you can send those to us separately.

Files which are less than 50MB can be attached to these support requests.
You can always upload larger files here:
https://skyline.ms/files.url
-- Nick