the problem of merging skyline documents with one raw data in different spectral libraries

the problem of merging skyline documents with one raw data in different spectral libraries zhao  2023-01-19 19:15

Suppose I have a raw data, named N1, which generates 300 sky files in 300 spectral libraries. How should I merge these 300 sky files? I try import-document and set it to merge with existing results by duplicate name, but the new results after import have no peak. I want to ask how to merge the sky files of different spectral libraries.
best wishes.

Nick Shulman responded:  2023-01-19 20:33
If you send us some of your Skyline documents we will probably be able to figure out what is going wrong.
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 and extracted chromatograms.
Files which are less than 50MB can be attached to this support request. You can upload larger (or smaller) files here:
We probably only need to see a few of your Skyline documents but if you want to send us all 300, that's fine too.

In my experience, "File > Import > Document" sometimes does the right thing, but more often than not it does something weird like you are describing.

An alternative to merging your Skyline documents would be to just upload them all up to

Panorama is a great place to store your Skyline documents, and I believe Panorama has some features to let you see results across multiple Skyline documents.
-- Nick
zhao responded:  2023-01-19 23:46
Hello, Nick
In order to describe my problem more conveniently, I uploaded the pptx file and two sky files I have another question to ask. The size of the cache file (skyd) generated by the sky file is very large. Even if I try edit-manage result-minimize, the file is still very large. Is this normal in DIA data?
Nick Shulman responded:  2023-01-22 15:45
Thank you for uploading that zip file.
Unfortunately, there are a few files missing such as the spectral library and background proteome files. Also, I see there were some .skyd files in there, but I am not sure whether those .skyd files are the ones that belong to the .sky files.

It would be very helpful if you could use the Skyline menu item "File > Share" to create two files and send me those two files.
When you use the "File > Share" menu item, Skyline puts all of the necessary files into one file. If you try to put the files into a .zip file yourself, you will probably forget to include some necessary files, so it's nearly always best to use the "File > Share" menu item when you want to send a document.

You can upload those files here:

The .skyd file contains the data for the extracted chromatograms. The menu item "Edit > Manage Results > Minimize" is useful if you have deleted a lot of peptides from your document. If you have deleted peptides from your document, the chromatogram data will remain in the .skyd file until you do "Edit > Manage Results > Minimize" or you do "Reimport" or something like that.
The other thing that you can do in the Minimize Results dialog is tell Skyline to discard the parts of the chromatogram which are outside of the chosen peak. That is, if you choose "Limit noise to 1 minutes before and after the chromatogram peak" then Skyline will truncate the chromatogram so that it only extends one minute before and after the selected peak.
If you have not deleted a bunch of things from the document and you do not tell Skyline to truncate the chromatogram, then "Minimize Results" will not have a significant impact on the size of the .skyd file.
-- Nick