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No chromatograms when importing Spectronaut file into Skyline

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No chromatograms when importing Spectronaut file into Skyline tang yun  2025-03-31 18:33
 

Hi Skyline Team,
I was trying to import my Spectronaut report files into Skyline, but there is no chromatogram been showed.
In the report file, it contained "Modified Peptide Sequence" "Relative Intensity" "iRT" "Precursor m/z" and "Product m/z" as Skyline indicated in the error message. After I modified my .tsv file, the file is successfully imported, but chromatogram place is empty. And under the "View" tab, the chromatogram button is grey that I cannot select. Could you help me with it? Thanks!
 
 
Nick Shulman responded:  2025-03-31 19:30
I think you might just need to tell Skyline to extract chromatograms.

You can use the "File > Import > Results" menu item to tell Skyline to extract chromatograms from raw files.
If you do "File > Import > Peptide Search" the import peptide search wizard guides you through creating a spectral library, importing a FASTA file, and then extracting chromatograms.

If I remember correctly, "Import Assay Library" is almost the same as "Import Transition List" except that you also end up with an iRT database. You still need to tell Skyline to extract chromatograms.

If these instructions were not helpful then you should send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including spectral libraries, iRT databases and extracted chromatograms.

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