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How to export chromatograms with SkylineRunner.exe without raw files

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How to export chromatograms with SkylineRunner.exe without raw files joon-yong lee  2024-06-19 15:20
 

Hello,

I wonder how to simply export the chromatograms with the Skyline CLI using the sky and skyd files without raw files.

I could successfully export the chromatograms only using the skyline files without raw files in the Skyline GUI version. In the directory, there are sky, skyd, skyl, and sky.view files. But no raw files.

I tried the following command but it didn't work. I might need to specify the replicate file names to export the chromatograms from though.

SkylineRunner.exe --in=test.sky --chromatogram-file=test_xic.tsv --chromatogram-precursors -chromatogram-products --chromatogram-base-peaks --chromatogram-tics

Thank you in advance.
 
 
Nick Shulman responded:  2024-06-19 16:55
In the text that you pasted there, you only have one hyphen before "-chromatogram-products". There needs to be two hyphens there "--chromatogram-products".

By the way, a different way to export chromatograms is to create a custom report with the chromatogram data in it.

You can learn about custom reports here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

The columns with the chromatogram times and intensities are called "Raw Times" and "Raw Intensities".
You can use the binoculars button at the top of the Customize Report dialog to search for a column by name.

Then, once you have defined your report for Skyline you would use the "--report-name" and "--report-file" arguments to tell Skyline to export your report report to a file.
-- Nick
 
joon-yong lee responded:  2024-06-20 10:18
My bad. Everything works perfectly. And thank you for letting me know how to customize the report template.

- Joon