Hi D. Baker,

Ion mobility is not one of the built-in metrics in Panorama QC folders. But it should be possible to add it as a custom metric. The documentation for adding custom metrics can be found here: https://www.labkey.org/Documentation/wiki-page.view?name=premPanoConfigMetrics#define

You will first have to create a database query for the value you want to monitor in Panorama. I can help you write the query but I would have to know which value(s) from the Skyline document you would like to track. I see a couple of places in the Skyline document where ion mobility values are stored - MS1 ion mobility, fragment ion ion mobility. Do you have a Skyline report to view the values you are interested in? Having that report would help us identify the corresponding database columns in Panorama.

If you are able to share your Skyline document that would be great. You can create a shared zip file (File > Share) in Skyline and attach it to this message thread if the zip file is less than 50MB. Alternatively, you can upload the document to a folder in your project on PanoramaWeb. If you have a Skyline report you can choose to include it in the shared zip file from the Settings > Document Settings > Reports tab in Skyline.

Thanks,
Vagisha

However, I don't think we have a suitable IMS metric being created by Skyline at the moment. Unless you know of a value you can see in Skyline reports that you want to track. There is currently no IMS Error value. Nor does Skyline have a per-run estimate of the observed IMS value (inverse mobility or CCS). Though, these things have been requested.

This may be a little confusing. I see that Skyline has the report values:
Precursor Results.Collisional Cross Section
Precursor Results.Ion Mobility MS1
Precursor Results.Ion Mobility Fragment
Precursor Results.Ion Mobility Window
Precursor Results.Ion Mobility Units

These values are essentially all prediction values. The Collisional Cross Section value would typically come from a library, and the MS1 and Fragment values would get calibrated based on a function provided by the instrument vendor, but these are all still about where Skyline extracted signal from the spectra. There is currently know information in the report about observed signal in the IMS dimension, the way that Mass Error works in the m/z dimension.

Am I making sense? I think you would need to wait for the Skyline Team to implement some kind of Ion Mobility Error or Observed Ion Mobility [value] fields to have something to track.

I have added a reference to this thread to our issues list where we have an issue about implementing Ion Mobility Error.

https://skyline.ms/issues/home/issues/details.view?issueId=774