Skyline supports commonly used a, b, c, x, y, z ion types with masses calculated according to the Biemann classification . While sufficient for most proteomics experiments, EAD (electron assisted dissociation) and related ionization methods produce some unusual ions that were impossible to track, specifically, z+1 radical ion and z+2 even electron ion. Skyline now supports these ion types starting from version 126.96.36.1994.
According to the de-facto standard in the literature, the z• and z’ notation is used for the z+1 radical ion and z+2 ion accordingly. Skyline uses it consistently across the UI in the chromatogram, mass-spectra and the targets tree. The library and full scan spectrum viewers have menu items to enable corresponding peak annotations.
Since the • in z• is not a character that is easy to type on a standard keyboard, aliases were introduced to facilitate user input. A couple of places where the aliases are used are the Find function of the ion picker list and the Filter tab of the Transition Settings dialog. z. or z* can be used for z• ions and z’ or z” for z’ ions.