Electron transfer dissociation facilitates sequencing of adenosine diphosphate-ribosylated peptides

Covalent adenosine diphosphate (ADP)-ribosylation of proteins is a post-translational modification that can occur both enzymatically and nonenzymatically and has been linked to many biological processes, such as the DNA damage and response mechanisms. Although the biochemistry of protein ADP-ribosylation has been extensively studied, the identification of physiological substrates remains a significant challenge due to inadequate tools for characterizing these modified peptides. Here we show that the use of electron transfer dissociation (ETD) greatly simplifies the mass spectrometric (MS) sequencing of ADP-ribosylated peptides over the conventional collisionally activated dissociation (CAD) approach. ETD sequencing of ADP-ribosylated peptides can be performed within a time scale compatible with nanoflow liquid chromatography and should prove useful for high-throughput large-scale studies on this unique class of modified peptides.