Will,

I think this will work if you go to "Edit > Manage Results" and push the "Rescore" button.
The latest versions of Skyline-daily store a little more information about the peaks that were originally chosen by Skyline during chromatogram extraction.
When that information is not there, the retention time alignment does not work at all.
The bug is that that extra information should not be required in the case where you have an iRT database with iRT standards.
I'll try to fix this in an upcoming release of Skyline-daily but, for now, the "Rescore" button should make things work for you.

If the "Rescore" button does not fix things then it means something else is going wrong and you should send me your Skyline document.
-- Nick

Hi Nick,

I'm not sure I understand. I don't want to re-score the peaks, because this will change the integration boundaries, right? I've attached the Skyline file for you to take a look. Thanks!

Will

Hi Nick,

I'm not sure I understand. I don't want to re-score the peaks, because this will change the integration boundaries, right? I've attached the Skyline file for you to take a look. Thanks!

Will

"Rescore" will not change the chosen peak boundaries.
It causes Skyline to go through the process of detecting peaks. Skyline will end up detecting exactly the same set of candidate peaks as it did before. Skyline will not move any manually adjusted peak boundaries.
Both "rescore" and "reimport" will not move manually adjusted peak boundaries.
"Rescore" is much faster than "reimport" because Skyline does not go through the process of extracting chromatograms. It just does the peak detection step.

I have also uploaded a special build of Skyline-daily which fixes this issue which you can install from here:
https://proteome.gs.washington.edu/~nicksh/SpecialSkylines/PeakImputation/

-- Nick

By the way, if you ever do happen to want Skyline to move all of your peak boundaries, the way to do that is to go to:
Refine > Reintegrate
and check the "Overwrite manual peaks" checkbox.

All of the other sorts of things like "Edit > Manage Results > Reimport" or "Edit > Manage Results > Rescore" or "Refine > Reintegrate" without checking that checkbox are not supposed to move peak boundaries that have been moved after Skyline chose them (i.e. peak boundaries that have been manually adjusted by a human or imported with "File > Import > Peak Boundaries" etc.)

-- Nick

okay great. The rescore trick worked for the display. I also checked that the native file itself opens in the current released Skyline 25.1. I can use the workaround if I need 'daily' until the next daily release. Thanks also for the explanation for rescore versus reintegrate.

Cheers

W