Characterization of top-down ETD in a travelling-wave ion guide

Top-down sequencing methods are becoming increasingly relevant for protein characterization, in particular electron capture (ECD) and electron transfer dissociation (ETD) which allow for extensive backbone cleavage with minimal side reactions. The ability to obtain sequence-specific fragments while maintaining aspects of the higher-order structure, as well as the position of deuterium labels in H/D exchange, has attracted interest from scientists in the field of structural proteomics. Recently, ETD has also been combined with ion mobility on commercially available quadrupole/time-of-flight instruments, and this implementation paves the way to novel structural studies and investigation of the ETD process itself. In the current work, we investigate the use of ETD for fragmentation of standard peptides and proteins and provide a detailed description of the effect of the parameters controlling the time and efficiency of the reaction. We also highlight how the combination with ion mobility separation after electron transfer provides extended analytical benefits, such as assignment of fragments to a specific charge-reduced state of the precursor.