FAIMS unit on Thermo Lumos

FAIMS unit on Thermo Lumos erik.soderblom  2019-11-20

Hi Skyline Team! I wanted to "bump" a thread entitled “Optimizing FAIMS on new Thermo instruments” from Martijn van Duijn back in September. We are now in the same boat (acquired a shiny new FAIMS device for our Lumos!) and at this point we just want to incorporate the data (say, 3 different CVs across 7 different peptides) into Skyline from our normal system suitability PRM acquisitions. I see where compensation voltage is a selectable unit under the ion mobility settings, but it doesn't look like Skyline is able to extract data for a single ("best") CV in the chromatogram view. Is this possible with current Skyline Daily ( yet?

Brian Pratt responded:  2019-11-20

Hi Erik,

If I understand what you're asking for, you'd like Skyline to be able to automatically determine which available CV is ideal for each precursor, then ignore the other CV ranges when extracting chromatograms.

Skyline does have this capability (see the tutorial at https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_ims ) although I am not certain that it has been used with FAIMS data yet. Have you tried it? If you find it doesn't work then let's get your data in here and we'll see what needs to be done.


Brian Pratt