Dear Skyline team,
one major pain point for my workflows manifests as follows:
When one enables further transitions for a precursor that already has a peak picked, those transitions would not have any extracted data, yet.
So I then reimport the MS data (Orbitrap full MS2, centroided extraction) in order to extract the data.
The transition is then displayed in the XIC successfully.
Yet, none of the quantifications or dotp information for the peak will adapt to the new data. In my understanding, the (manually picked) peaks should stay in terms of positioning, but all the extracted area measurements, dotp etc should update according to the new XIC data.
The same (presumably) effect comes into play, when one adjusts the extraction ppm limit, which could have major effects on the XIC (as is visible), but the summary data again is not updated.
This forces me to either run full peak reintegration, losing all manually picked peaks, or delete the .skyd, which causes deselected peaks to be picked automatically again. Both of these options are quite burdensome with fully curated files.
I am using Skyline 18.104.22.168
I just tried to set up a minimal example using a simple small molecule setup.
I am attaching a minimal skyline and rawfile. There is only one transition with a manually picked peak (just some noise for this example).
If you open that file, you can take note of the transition area (17608) extracted at 1 ppm.
You can adjust the extraction ppm to 1000 and attempt reimport (via edit -> manage results).
This to me doesn't update the XIC at all (a separate bug?). But upon saving and reopening, the XIC is updated to reflect the 1000ppm.
The transition area now is still 17608 and only updates when playing around manually with the selected peak limits.
I feel that this is likely very much unintended behavior and hope that this description will be helpful.
Please let me know if any further info is needed.