Skyline not recognizing FIAMS CV rough tune data cmwats2  2020-03-03


I used Skyline to export SRM transition list for compensation voltage rough tune. I acquired the data on an Altis instrument. I imported the data selecting optimizing compensation voltage -> rough tune. I attached an image of the imported data. However, when I try to make an optimization library containing the peptides and best CVs, skyline says there are no new optimizations. I can successfully create the optimization library for collision energies. What am I missing for Skyline to select the optimal FAIMS CV for my peptides? I cannot make a medium or fine tune method because I do not have the rough tune data.

Thanks in advance,

Nick Shulman responded:  2020-03-03

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:

-- Nick
Kaipo responded:  2020-03-04
Hi Caroline,

You can only add compensation voltages to an optimization library with fine tune values.

With your current document, you can export a compensation voltage medium tune transition list. Once that data is imported, you should be able to export the fine tune transition list.

cmwats2 responded:  2020-03-05
When I try to export a medium tune all the compensation voltages in the transition list are 0. Please see the attached file. This is why I thought I need an optimization library for the rough. My real issue is I need to do medium and fine tunes on my data but I cannot get skyline to export transition lists for that.
Kaipo responded:  2020-03-06
Hi Caroline,

Sorry about that, it looks like Skyline does not work properly with negative compensation voltages. If the compensation voltage is negative, it will export a zero in its place. I will fix this for the next Skyline-daily release.