Removing automatically-loaded library

Removing automatically-loaded library bsundberg  2021-12-01

Hello Skyline Team,
I received a Skyline document from Pierce along with their 7x5 synthetic peptide mix for evaluating system suitability data from those peptides. I would like everyone in our group to be putting data into this document, so it should be as uncomplicated as possible to use. However, the document automatically expects a spectral library that isn't provided, and Pierce's instructions tell you to just ignore the pop-up message about the missing library. The problem is that in the absence of the library Skyline does not import the data completely, resulting in the message "chromatographic information unavailable". Deselecting, removing, or resetting the library in Peptide Settings resolves the issue temporarily, but upon importing more data or making a copy of the document, the library shows up again! How do I permanently remove this "missing library" from the document? Problematic document is attached. Thanks for your help!

Nick Shulman responded:  2021-12-01
I know that Skyline has a bug in it where things do not work correctly if Skyline tells you a library is missing and you choose to open the document anyway.

I am supposed to fix this bug (thanks for reminding me).

However, I have never seen the behavior that you are describing where the library "comes back" after you have removed it. The file which you attached does not appear to think it has a library, and I cannot think of any way in Skyline that the library would somehow appear as a result of importing more chromatograms. (when you say "making a copy of the document" do you mean "Save As", or are you making a copy in some other way?)

Could you send me the original Skyline document that Pierce sent you? It could be that if I opened that original document I would be able to get my Skyline into the same state that it is on your computer, with a zombie Library somewhere.
-- Nick
bsundberg responded:  2021-12-01
The zombie library does not seem to be an issue with the Pierce document, so maybe I messed something up in my Skyline document along the way?

The zombie library reappears in copies made through both "Save As" duplication within Skyline and copy-paste in the file explorer, though it will also reappear just by closing the file and reopening it. I attached some screenshots of the peptide settings: (1) with the zombie present, (2) after the zombie is removed, (3) from zombie-eradicated file after duplication (File > Save As...), then also (4) upon reopening the zombie-eradicated file.

P.S. We just decided to go with a different sys suit mix, so I won't be continuing with this file anyway, but I guess at least the issue has been documented? It seems like I can permanently remove the library from the other Skyline files on my computer without issue. Still, I'd be happy to continue any testing or troubleshooting on this is you think it would be useful for Skyline overall.
Nick Shulman responded:  2021-12-01
Thank you for sending that new Skyline document.

Yes, that document has a library in it called "6P_PRTC" which you will indeed have a hard time removing.

If you want to remove that library from the document, what you need to do is point Skyline at some other .blib file on your computer when Skyline asks you where to find the library "6P_PRTC".
That is, when you open the document, and Skyline says, "This document requires the '6P_PRTC' Spectral Library", you should click the "Browse" button and point Skyline at some other .blib file that you have on your computer somewhere.
If you do that, then you will be able to go to "Settings > Peptide Settings > Library" and you will be able to uncheck the box next to "6P_PRTC".

Your screenshots shows a library whose name starts with "MIDAS_". That library is not the one which is causing you problems, but I can imagine that when it is there, it exacerbates the symptoms of the missing "6P_PRTC" library. That is, Skyline is willing to allow you to extract chromatograms when the 6P_PRTC library is missing, and the document has zero other libraries. But, if there is a missing library and there is at least one other library that could actually be found, you are prevented from extracting chromatograms.

By the way, the MIDAS library gets added to your document when import SCIEX wiff files which contain MIDAS spectra.

I will try to fix Skyline so that it is easier to remove the missing library without having to do the workaround of pointing Skyline at a different .blib file.
-- Nick
bsundberg responded:  2021-12-01
Okay, this is interesting! And I'm glad there is a logical explanation behind the weirdness.

Thanks for your help and instruction!