Thanks for trying the special Skyline build to run Carafe. This is an "unofficial" version special preview build with Carafe functionality. It is still being tested and perfected, your patience with any bugs you may encounter is appreciated. If you are able, please share your Skyline document, the training mzML file and the DIA-NN report and I would be glad to investigate these issues further, using the latest code of this branch, still under development.

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

Thank you,
-David

Terminal modification is not supported:Ethyl of protein N-term

This is not an error. It is just a note to indicate N-term modification is not supported yet.

If DIA-NN version v2.2.0 is used, --export-quant is needed to add to the command line of DIA-NN search to export "Ms2.Scan" in the main report "report.parquet". If you run DIA-NN v2.2.0 through its GUI, you can add this parameter as shown in the figure attached.

thanks for that! it was indeed with DIA-NN V2.2. I have updated the parameters but now I get the issue that it says "No ions matched!"

It's possible that some ms2 scans (not many) at apex we extract for use for fine-tuning don't have any matches to some detected peptides. If that happens, you will see "No ions matched!" from the command line output. The corresponding peptide detections will not be used for training.

If you could share the two input files with me, I’d be happy to take a look and check for any issues.