Exporting data

Exporting data herath lakmini senavirathna  2023-08-28 11:14

Hi Skyline Team,

I have an issue with exporting the Excel file for peptide quantification from the Skyline file for a large number of data set (the number of results/raw files imported are close to 100). The generated Excel file cannot be opened or all the data are not exported as the number of rows that a Excel file can have passed the maximum limit. So, could please advise me on how to export all data? I am using iRT calibration as well.


Nick Shulman responded:  2023-08-28 11:50
Can you send us the file that you exported from Skyline? I might be able to figure out what went wrong.

It also might be helpful if you could 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.
If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:

It might also be helpful if you could send us your report definition.
One way to send us the report definition would be to include it in the Skyline document. So, for that, before you do the "File > Share" thing above, you would go to "Settings > Document Settings" and on the "Reports" tab, you would check the checkbox next to the report name that you were using.

-- Nick