No transitions visible since latest Skyline daily update

support
No transitions visible since latest Skyline daily update lena reimann  2019-09-25
 

Dear Skyline team,

I updated our Skyline daily version to 19.1.1.248 yesterday. Since this time point, we are no longer able to see any transitions in our AutoQC pipeline or following manual data import into Skyline. If I check for the transitions manually with Xcalibur or use older Skyline daily versions e.g. 19.0.9.190 all the transitions are visible.
Is there anything I can do to recover the visibility/import of the transitions? At the moment they are also not imported into PanoramaWeb, so we are lacking some valuable information about our instument performance.

Thanks for your help and providing this great software,
Lena

 
 
Nick Shulman responded:  2019-09-25
Can you send us your Skyline document?

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 that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:
https://skyline.ms/files.url

-- Nick
 
lena reimann responded:  2019-09-25
Please find attached the .zip file containing the Skyline document. You will see that there are all transitions present exept for the last imported file. Have some settings changed during the updateing process? I checked the transition settings and they seemed the same as before to me.

Thanks, Lena
 
Nick Shulman responded:  2019-09-25
Can you send me the file "QEplus024857.raw"?

I will try to figure out why Skyline does not seem to find any MS2 scans in that file which match your targets.
-- Nick
 
lena reimann responded:  2019-09-25
Yes, uploaded it to the file sharing folder.

Thanks, Lena
 
Nick Shulman responded:  2019-09-25
Thanks for sending that .raw file.

We made some changes in the latest update of Skyline-Daily to enable extracting chromatograms from MS3 data. As part of that change, Skyline now pays attention to which MS level a particular precursor isolation happened on.
For some reason, your MS2 scans say that the precursor isolation happened at the MS2 level (which does not make sense) and so Skyline does not properly use those MS2 scans to extract chromatograms.

I will ask some other people stuff and figure out what is going on.
-- Nick
 
Nick Shulman responded:  2019-09-25
This bug will be fixed in the next update of Skyline-Daily.

The current version of Skyline-Daily does not properly handle MS2 scans that have more than one isolation window. For example, you have scans that isolate 582.31897 and 751.81052. (These types of scans are sometimes called "MSX").

We usually release new updates of Skyline-Daily every few weeks. In the meantime, you might want to roll back to the previous release of Skyline-Daily. You can do that in Control Panel Programs and Features. If you press the "Uninstall/Change" button, Windows will usually give you the option to "Restore the application to its previous state".

Thanks for reporting this bug!
-- Nick