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Polarity mismatch error during import of polarity-switching raw file

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Polarity mismatch error during import of polarity-switching raw file p ivanov  2025-03-01 00:44
 

Greetings,

Firstly, I want to praise your efforts in creating this application, it is powerful and has quite clear documentation.
Still, I have encoutered problem almost immediately. Analysis was performed on Shimadzu LCMS-8030 with ESI ionisation in both negative and positive modes (centroided). Generic output of Shimadzu was converted to .mzML format. After pasting a transition list (I tried different options - attached) and after importing raw results I get an error: At 11:22:
Failed importing results file 'D:\Program Files\skyline\data\mzML-F10_flav_MRM_5-95_004.mzML'.
polarity mismatch (full text is attached).

I tried to change some transition options but without any success (current settings with .sky file will be attached in 'file sharing' with name "flavonoids_refined_table_gao_ren.sky.zip").
In this .zip I also attached one of .raw file, if it would be of any help

My system: Windows 20 (64-bit) Home, version of Skyline: (64-bit) 24.1.0.414 (5b5ea5889c)

With gratitude,
Paul I.
 
 
Brian Pratt responded:  2025-03-01 17:06

Hi Paul,

Thanks for the report.

I can reproduce the problem with the files provided, thanks. We will investigate and report back.

I would be curious to see the unconverted data, too. Skyline should be able to read that directly, if that isn't the case I'd like to understand why. I did not see it in the zip file.

Thanks for using the Skyline support board!

Brian Pratt
 
p ivanov responded:  2025-03-03 08:54

Thanks for fast response!

Yes, you are quite right and Skyline managed to work with .lcd files, it's alleviating. I will attach one of them to "file sharing".
Explanation for this lies in troubles with interlaboratory communication - as I was told .mzML files should have been OK (and also less massive).

Still, they are not working and it will be of much consideration, if you can find out why.

Thanks again!
 
Brian Pratt responded:  2025-03-03 12:52

Thanks again for providing the files. The problem will be corrected in the next Skyline-Daily release.

.mzML files should have been OK (and also less massive).

Those are very strange mzML files, by the way. When I convert to mzML using msconvert the files are much smaller - by a factor of 173x (!).

The .mzML files you provided do succeed in my corrected build of Skyline, but they provide rather different results than the .lcd files, or .mzML files produced using msconvert. You might want to investigate with the lab that provided them.

Regardless, they did point out a latent problem with Skyline and I thank you for providing them.

Best,

Brian Pratt