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Cannot import negative mode small molecule data from Waters instrument

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Cannot import negative mode small molecule data from Waters instrument sgaunitz  2026-02-24 02:13
 

I have in Skyline 25.1 previously successfully analyzed small molecules in negative mode Orbitrap full scan raw data.
Now I want to transition to Waters single ion reaction (SIR) analysis in negative mode. When I try to import data into Skyline I get the error message:

"Failed importing results file '(---)\SSTallatoppar_0_3mm_MRM_3mm_forkolonn12.raw'.
This document contains only negative ion mode transitions, and the imported file contains only positive ion mode data so nothing can be loaded."

I tried to convert to the Waters raw file to mzml and specifying the polarity mode as negative but I get the same error message. How do I proceed?

best,

Stefan
 
 
Nick Shulman responded:  2026-02-24 07:14
I believe this will work for you if you use Skyline-daily instead of Skyline 25.1.

You can install Skyline-daily by clicking on the "Skyline-daily (beta)" button on the main Skyline web page:
https://skyline.ms/home/software/Skyline/project-begin.view

I am not sure exactly why Skyline 25.1 does not recognize your chromatograms as being negative mode, but the problem seems to have been fixed in Skyline-daily.

We will be releasing Skyline 26.1 in a week or two and when we do that, Skyline 26.1 will also be able to handle your data.
-- Nick
 
sgaunitz responded:  2026-02-26 02:19
It worked using the daily-version!
Thanks!

Stefan