Combining Files without Reintegration

Combining Files without Reintegration Will Thompson  2023-11-14 07:50

Dear Skyline team, when building a skyline compound library, I'd like to use the file/import/document function to combine skyline files. The trick is that when combining the files I want Skyline to merge the compounds that are the same, but not re-integrate all the other runs for the compounds that are different (because, those compounds don't actually exist in many samples). However, using I can't seem to get this to happen; when I use the import/document function it always interrogates all the files for all the compounds, no matter which options I select. Can someone take a look at this using the two files I have attached? To summarize, functionality I want:

Combine Files
Collapse same/shared analytes
Perform no additional re-integration (leave compounds that are unique to each file alone, and don't try to find peaks in the other raw data).

Is this possible?



Nick Shulman responded:  2023-11-14 16:22
I think the reason that you are not getting the results that you expect is that both of these Skyline documents used to contain more molecules than what you are seeing in the Targets tree, and the .skyd file still contains zombie chromatograms from these deleted molecules.

You should go to:
Edit > Manage Results
and push the "Minimize" button, make sure that "Discard unused chromatograms" is checked and then push "Minimize in place".

After you have discarded unused chromatograms from both of these documents, you can do "File > Import > Document".
For the molecules that can be found in only one of the two documents, there will be no extracted chromatograms for the replicates from the other document, so there will be nothing for Skyline to look for peaks in, and so the peak areas will be null as you expect.

-- Nick
Will Thompson responded:  2023-11-15 04:12
Aha! Flummoxed by the Zombie Chromatograms!

Thanks Nick. I forgot about that step.