Ion Mobility Separation (IMS) Data
Skyline supports IMS data for Waters, Agilent and Bruker instruments. Using an ion mobility predictor can help Skyline ignore unwanted signals and improve data quality. By specifying the predicted ion mobility for each molecule of interest you can tell Skyline to ignore other scans that might contribute noise.
To add or change an ion mobility predictor, use the Settings|Peptide Settings menu item and select the Prediction tab, then the Ion Mobility Predictor button to bring up the Ion Mobility Predictor table editor.
The easiest way to set up an ion mobility predictor table is to start with a Skyline document with imported results, then use the "Use Results" button in the Ion Mobility Predictor editor. This simply scans the existing imported results and determines the ion mobility value of the scan containing the most intense peak. Once you have that, you can reimport the data and Skyline can ignore scans at the proper retention time but wrong ion mobility.
There is a risk, of course, that the most intense peak at a given retention time isn't actually that of the precursor you are interested in, in which case you will be making the noise situation worse instead of better. The ideal way to use this training feature is with simple training sets that elute one precursor at a time. If you do not have that capability then you should go through and verify the ion mobility selections manually using the chromatogram viewer's intensity heat map of mz vs ion mobility.