Share minimum does no longer work with v 4.1

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Share minimum does no longer work with v 4.1 dkueltz  2018-01-21 22:26
 
Hi Nick, Brendan,
I am trying to share: minimal a skyline file but it does no longer work with version 4.1. I always get the same error (The given key was not present in the dictionary). This happens with both the full version and Skyline daily (both 4.1). The error is attached as a screenshot. I checked that the referenced paths to the irtDB, protdb, and blib files are all correct - so broken paths to required files cannot be the reason. The error mentions something about small molecules even though this skyline document does not contain small molecule data. Thanks for taking a look at this!
Dietmar
 
 
Nick Shulman responded:  2018-01-21 23:37
I have not seen that error before. Can you send us your Skyline document?
I imagine the "share complete" option still works, so you can do:
File > Share > Complete
and send us that .zip file. If it is less than 50MB then you can attach that .zip file to this support request. Otherwise, you can upload it here:
https://skyline.ms/files.url

It looks like the error is caused by Skyline being confused about which library one of your precursors is associated with.

That is, if you go to the Document Grid and choose the "Precursors" view, then I would expect to find that the "Library Name" column has at least one entry which does not match the name of any of the libraries that you are using.
(I might be wrong about this diagnosis-- it will be easy to figure out what is going wrong when I see your .sky.zip, but it might not be clear how it got that way).
 
dkueltz responded:  2018-01-22 18:13
Hi Nick, your diagnosis was correct. I did not end up uploading the docuemnt since the complete zip is >1GB. But when looking at the precursor table in document grids half of the peptides had a different library assigned. It turned out that these were the decoy peptides. So apparently I changed the library link location after the decoy peptides had been generated but then the old library still remained attached to the decoy peptides and never got updated for those. Deleting the decoy peptides resolved the issue.
Thanks!
Dietmar