Skyline supports IMS data for Waters, Agilent, Thermo (FAIMS) and Bruker instruments. By specifying the ion mobility for each precursor ion of interest you can tell Skyline to ignore scans that might contribute noise, and thus improve the quality of extracted chromatograms. The Ion Mobility Spectrum Filtering tutorial provides examples and more detail.
Ion mobility values may be specified in Ion Mobility libraries, or defined explicitly in transition list imports, and may also be found in spectral libraries (for the latter, make sure to check the "Use spectral library ion mobility values when present" box in the Ion Mobility tab of the Transition Settings dialog). The order of precedence is: explicit values, Ion Mobility Library values, Spectral Library values.
You will notice that an ion mobility is commonly expressed as a Collision Cross Section (CCS) value and an ion mobility value. It's important to understand that the CCS value takes priority: different raw data files may contain different CCS->mobility calibrations, so the actual ion mobility filter value for a chromatogram extraction is always derived from the CCS value when available. Thus, if you want to experiment with adjusting ion mobility values for chromatogram extraction, it's import to either adjust CCS rather than ion mobility, or to clear the CCS setting so that your adjusted ion mobility value is the one that gets used.
To add or modify an ion mobility library, use the Settings|Transition Settings menu item and select the Ion Mobility tab, then use the "Ion Mobility Library" drop down menu to bring up the Ion Mobility Library editor.
The easiest way to set up an ion mobility library is to start with a Skyline document with imported results, then use the "Use Results" button in the Ion Mobility Library 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 Full Scan chromatogram viewer's intensity heat map of mz vs ion mobility.
You can also set explicit ion mobility values for small molecule precursors using the right-click menu in the Targets window. This can also be done in the Document Grid, so it's possible for peptide precursors as well.