CCS Values from Bruker DDA-PASEF data

CCS Values from Bruker DDA-PASEF data Premy  2022-08-17

Hi there!

I am working with the Bruker timsTOF Pro instrument and have collected DDA-PASEF for a set of lipid standards. After using LipidCreator to create a transition list, replicate data from a dilution series was analyzed.

When adding "Ion Mobility MS1" to the Document Grid, the column shows up as NAN for every row. I'm not sure if I've missed something in the document setup?

Any help would be appreciated and thank you in advance!

Brian Pratt responded:  2022-08-17

That's a value that you have to provide to Skyline so it knows what IM values to use for each precursor during chromatogram extraction. I don't think that's something LipidCreator supplies, so you'll want to train an ion mobility library then re-extract your chromatograms.

More details here:

Thanks for using the Skyline support board!

Brian Pratt