Merging two documents

Merging two documents Michael Cundell  2022-01-12

I am having trouble merging two documents in Skyline (64-bit) (f09d9bed5) which is probably a result of how I created the two documents:

  1. I had a document with all peptides/transitions of interest in it.
  2. I then imported the raw files.
  3. I then copied the three files .sky, .sky.view and .skyd and shared those with a colleague.
  4. We then both adjusted peak integration boundaries and removed some of the light peptide channels by right clicking chromatograms and choosing 'remove peak' for specific replicates. Generally we kept all heavy label channels, but sometimes we removed these peaks also.
    My colleague started from the top, i started from the bottom.
  5. When we met halfway we both stopped.
  6. we both copied the documents to a separate folder (in case of issues) and each deleted peptides whose peak boundaries were not adjusted in our respective documents.

From this point, is there a way to merge these two documents (referred to as A and B below)?

I tried file > import > Document and select "merge with existing results by replicate name". When i merge A with B, the missing peptides in A are added from B to the targets pane, but the adjusted peak boundaries and removed light labels are not brought over into A from B. Instead, I just get the original skyline peak boundaries created at import in step 2 above (I presume this is because they still reside in skyd in document A). If I do "add new replicates" instead all peak boundaries and selections are brought over from B into A fine, but this just duplicates the replicates (which are identical in both documents).

I also tried exporting the peak boundaries from A and B, then concatenated those lists together in excel and reimported with file > import > peak boundaries. This gave the right windows, but all peaks had both heavy and light labels turned on (it didnt take into account we would like to preserve where we have removed a light label, to keep that light label off/removed from the specific replicates).

Probably the simplest solution is to just keep the documents separate and export the peptide results from each file and merge the two output CSVs. But it would be good to know if I am missing something.

Thank you for your help and a great tool.

Best wishes,


Nick Shulman responded:  2022-01-12
Can you send us your two Skyline documents?
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If those .zip files are less than 50MB you can attach them to this support request.
Otherwise, you can upload them here:

We would expect that "File > Import > Document" would be the way that you should merge these two documents. It sounds like "Import Document" is not preserving peaks that you have removed. This might indicate that there is a much deeper bug happening in Skyline where removed peaks might be reappearing when you do other changes, such as just changing settings, so we would definitely want to take a look at this and make sure we understand what is going on.

In terms of different way of merging the two files, I imagine you could open the two .sky files up in two text editors. Skyline documents are stored as XML, and it would be pretty straightforward to copy peptides from one document to the other in a text editor.

But, please send us your Skyline documents. I will figure out what is going on.
-- Nick
Michael Cundell responded:  2022-01-13
I am having problems sharing the documents due to company IT restrictions. Please can you email me or provide an email address so that i can send a onedrive link through to you which I am advised should work.

I created two new documents that I can share to highlight the reproducible issue. These are SP_A and SP_B, they were created identically to how I described in my original post. There are two replicates. I removed light labels from both in both documents.

When you merge SP_B into SP_A, you can see that:
1. light labels are included
2. Worse, peak selection boundaries revert away from what was chosen in SP_B, back to the 'original peak'

I also created the documents a different way:
1. add 2 peptides to document
2. save
3. copy document to create SP_A_2 and SP_B_2
4. open both documents and delete 1 peptide from each
5. import data separately into each document and save

When you try and import SP_B_2 into SP_A_2, the peptide is added to the targets pane, but not chromatogram data is brought over.
Nick Shulman responded:  2022-01-13
Thank you for sending me your Skyline documents.
I think it would be really hard for us to fix the behavior of "Import Document" so that it preserves the peak boundaries and the peaks that were removed.
The usual way that we recommend dealing with peak boundaries moving in cases like this is that you export the "Peak Boundaries" report to a .csv file, and then use the "Import > Peak Boundaries" menu item to read that CSV file.
Unfortunately, when you do "Import > Peak Boundaries", it does not have the ability to distinguish between different "light" and "heavy".

One thing that you could conceivably do is create a report with the columns "Total Area" and "Precursor Replicate Note" in it. You could filter for the rows where "Total Area" "Is Blank", and then set the "Precursor Replicate Note" in all of those rows to "Missing".
Unfortunately, when you import document B into document A, those Precursor Replicate Note values will all be lost.
But, fortunately, you can use the "File > Export > Annotations" menu item to export the Precursor Replicate Note's from document B.
Then, in your merged document, you can use the menu item "File > Import > Annotations" to import those exported annotations.
Then, you can filter your report to find the rows where Precursor Replicate Note is "Missing", select all of the rows and use the "Actions" dropdown button at the top of the Document Grid to "Remove Precursor Peaks".

In email, I also sent you instructions for how to use a text editor to copy/paste all of the proteins from one document to another, which might be easier than Export/Import annotations & Remove Precursor Peaks.
-- Nick