The best way to send Skyline documents is to use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

We will probably also need to see your raw mass spec data files. The Share Document dialog gives you the option to include the raw data files in the .zip or you can send them 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

Can you send us one of your .mzML files such as:
studentsProjects2_charlotte_PLA_MS-LIPIDS-4@fEPP_STXr05_STXp012-PQC_20.mzML

If that file is less than 50MB you can attach it to this support request. If it is larger than that you can upload it here:
https://skyline.ms/files.url

One difference that I see between your two Skyline documents is that the GUI one used the July 25rh official version of Skyline-daily 25.1.1.206, whereas the command-line one used an unofficial build of Skyline made from the current sources in the master branch. I cannot think of anything that might have changed in the code in the last month which would have affected reading SRM chromatograms.

I see that these molecules with missing chromatograms do have the "Explicit Retention Time" set. The Explicit Retention Time can often cause you to see the "Chromatogram Information Unavailable" message because Skyline will avoid using SRM chromatograms which do not overlap with the explicit retention time. I cannot think of a reason that this behavior would only impact the command-line version, so it might not be related to the behavior you are seeing.

After I see one of your .mzML files it will probably be easier to figure out what is going on.
-- Nick

Hi Nick,

Thank you for your prompt replies.

Please find the attached mzml.

My only other thought is that the issue may arise because I am running skylineCmd through the latests Proteowizards Skyline Docker (Tag:skyline_25.1.0.224-519d29b). Note, I have tried older releases of the Docker image and still encounter the same issue.

Kind regards,
Harrison

Thank you for attaching that .mzML file.

Can you tell me what command-line you are giving to SkylineCmd.exe to tell it to import chromatograms?
-- Nick

This is the current command for the workflow

docker run --rm -v "%s:/data" proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses wine SkylineCmd \
      --dir=/data \
      --in=%s \
      --import-transition-list=%s \
      --import-all=%s \
      --import-peak-boundaries=%s \
      --save-settings --overwrite \
      --out=%s \
      --report-conflict-resolution=overwrite \
      --report-name=%s \
      --report-file=%s \
      --report-add=%s \
      --report-format=csv \
      --report-invariant \
      --chromatogram-file=%s \
      --chromatogram-precursors \
      --chromatogram-products \
      --chromatogram-base-peaks \
      --chromatogram-tics'"

import chromatograms is --import-all=path/to/folder (replaced with actual path)
Harry

Could you send me the Skyline document that you are referencing with the "--in=" parameter? (That's probably a small .sky file with nothing in it).

Also, you would not happen to have captured the text output of running your commands? That output will probably have a clue as to why some of these chromatograms are being skipped.

I might be able to figure out what is going on without this additional data, but it might help.
-- Nick

Here is the .sky file for "--in" and output from running the commands

--Harrison

The behavior seems to have something to do with the slash character in the molecule name. That seems to be getting changed into an underscore in the .skyd file. I am not sure where that might be happening or why you're seeing differences depending on how you execute Skyline.
I will continue investigating.
--Nick

I've removed all slash characters from the transition list, which has fixed the issue.

It's interesting how it only impacts the SkylineCmd.

--Harrison