CCS measured vs. CCS explicit (or library)

CCS measured vs. CCS explicit (or library) tim causon  2021-04-09 03:04

Skyline is doing a great job with filtering LC-IM-MS data, but we are looking for some improved reporting options.

  1. When we have a known set of target molecules to search for, we create a simple Skyline transition list for small molecules with: RT, Explicit CCS, molecular formula, and ion species.
  2. In CCS-calibrated files, the target CCS is converted to a target Drift Time, which does a great job filtering the results in the measurement files as we want it to.

However, the reporting options only allow the "Explicit CCS" to be reported (that is our "target value"). Other options available for reporting are identical or are the "target drift time" and not the "measured CCS". Note: "Measured drift time" is not as valuable as we may import data files with different CCS calibration functions applied.

Would it be possible to include an option to report the "Measured CCS" (i.e. calculated from the measured drift peak apex)? This would allow "CCS Error" to be reported in a similar way to "Mass Error PPM".

Nick Shulman responded:  2021-04-09 09:10
If you want to see the observed ion mobility value averaged across all of your replicates, you can use the new "Library Ion Mobility" column which is going to be available in the next update of Skyline-Daily (which will be available in less than a week).

The new Library Ion Mobility column will show the ion mobility value from your Ion Mobility Library (.imsdb) file.

You can tell Skyline to populate the .imsdb file with the observed ion mobility values in your Skyline document. To do this, go to:
Settings > Transition Settings > Ion Mobility > Ion Mobility Library > Add
create a .imsdb file, and then push the "Use Results" button to populate that .imsdb file with the ion mobility values in your document.

If you would like to see some screenshots of what the Library Ion Mobility column is going to look like in Skyline-Daily next week, you can see them here:

It would also be a good idea for us to add the Measured CCS and CCS Error values as you are suggesting (those things would go on the "Transition Result" object in the Document Grid). I imagine those new columns will appear in Skyline-Daily in early summer after we release Skyline 21.1.
-- Nick
lidia belova responded:  2021-12-15 07:29
Dear both,

I am starting to use Skyline for LC-IM-HRMS screening studies on small molecules. As Tim already mentioned, it is a great tool for data filtering. However, I faced the dame problem as Tim when trying to export the IM data for targeted compounds from my files. When using both a target list or a previously created library file, only the @Explicit CCS) (i.e. the value included in my target list or library) is reported and not the actual measured CCS of each data file.

Since some time has passed since the last posting here, is there now a way to export the measured CCS? Currently, I am using version 21.1.0.

Thank you very much in advance!
Nick Shulman responded:  2021-12-15 09:45
We have not added the peak apex CCS value to Skyline.
I have opened an Issue so that we do not forget about this:

We might be able to implement this feature in the next release cycle, but we might not. The tricky thing is figuring out how to add this extra peak information to the .skyd file without impacting the size of .skyd files which do not use ion mobility. Currently, Skyline does not have a way to store "optional" information in the .skyd file, so every new feature we add increases the size of everyone's .skyd file.
We hope to figure out a solution to this in the coming months.

Thanks for reminding us about this feature request.
-- Nick