Hi Ru,
It seems that you didn't originally include the missing ion y15++ when you first imported your data, which would certainly cause what you are seeing. In fact, what you are seeing would be expected in that case. Skyline only extracts the chromatograms in your targets list when you import a file.
So, the only surprising point is the comment that you tried to reload the file but it did not help. Everything up to that point is completely expected.
Your effort should be directed toward understanding why the "reload" did not have the expected impact of causing Skyline to include the y15++ ion in its extraction. I would probably try the following:
- Just close and re-open the file to see if it was an update problem where the re-import actually worked, but Skyline failed to notice the new chromatogram.
- Use Edit > Manage Results to Remove All replicates. Save the empty document. Reimport on file to see if the problem persists, which would be really surprising, but also very informative.
- Assuming the above did not reproduce the problem. Remove the one replicate again. Remove the y15++ ion and repeat your original steps to see if you can create a simplified set of steps that reproduce the problem with a single document.
Once you have narrowed down what exactly you did and where Skyline is failing to meet expectations, report back and we will want the minimal set of files you used to reproduce the problem.
Also, can you give more detail now on what method you used to "reload" the replicate you are showing? Did you fully remove it using Manage Results and then use File > Import > Results to add it back, or did you use the "Re-import" button in the Manage Results form? And what version of Skyline are you using? (see Help > About)
Thanks for the screenshots with your report and your appreciation of our work.
--Brendan