CCS calculation from mobility value and normalize/calibrate mobility across replicates

CCS calculation from mobility value and normalize/calibrate mobility across replicates madeline colley  2022-02-11


I am thoroughly enjoying the skyline small molecules course and found two features which would be nice to implement and help synergize data across many platforms (PASEF/DT/etc).

  1. Calculate CCS from mobility: Being able to import library data as 1/k0 or drift time and then use the vendor DLL to calculate the CCS from this would be a great diagnostic tool to figure out how CCS varies across instruments, labs, etc.

  2. Normalize/Calibrate mobility: Since there is drift over time, particularly from what I have seen in some open-access tims data, it would be great if skyline had a feature to realign/normalize 1/k0 or drift time based on a QC file, internal standard, etc. I know that I use the avanti CCS mix for lipidomics to help me see how far my data has moved (if it has) and I would like to be able to use these as a way to shift my mobiligram.

From this data we could also then calculate the required window for a given mobility rather than have a specific vendor setting based on the instrument.

Thank you!

Brian Pratt responded:  2022-02-15

Hi Madeline,

I'm glad you're enjoying Skyline. To your points:

  1. Skyline can do this already. If you have a replicate loaded, Skyline should show you (in the Document Grid) the calculated CCS for any given transition with a 1/K0 value, based on the calibration implemented by the vendor (typically encoded in the raw file itself, but in a manner unknown to Skyline).

  2. If you run a standard through Skyline (that is, not a lot of co-elution going on) without any ion mobility filtering enabled, Skyline can build an ion mobility library from observation of the IM peaks in the data. You could then compare those results to past measurements.

It's important to understand that Skyline really depends on the instrument for calibration - when given both a CCS and a mobility value, Skyline always uses the CCS value and relies on the vendor DLL to provide a mobility value from that. CCS is considered ground truth, independent of instrument, so perhaps we already have what you're looking for. Though, of course, CCS itself is actually dependent on machine conditions (gas type and pressure, etc) so that only gets you so far.

I hope this helps,

Brian Pratt