Overview

Skyline supports commonly used a, b, c, x, y, z ion types with masses calculated according to the Biemann classification [1]. 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[2]. Skyline now supports these ion types starting from version 21.2.1.404.

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.

References:

1. K. Biemann, Methods in Enzymology, 193, 886-887 (1990)
2. K.O. Zhurov et al., Chem. Soc. Rev., 42, 5014-5030 (2013)