Mass spectral feature analysis of ubiquitylated peptides provides insights into probing the dark ubiquitylome

Abstract Ubiquitylation is a structurally and functionally diverse post translational modification that involves the covalent attachment of the small protein ubiquitin to other protein substrates. Trypsin-based proteomics is the most common approach for globally identifying ubiquitylation sites. However, we estimate that such methods are unable to detect ~40% of ubiquitylation sites in the human proteome – i.e., “the dark ubiquitylome” – including many important for human health and disease. In this meta-analysis of three large ubiquitylomic datasets, we performed a series of bioinformatic analyses to assess experimental features that could aid in uniquely identifying site-specific ubiquitylation events. Spectral predictions from Prosit were compared to experimental spectra of tryptic ubiquitylated peptides, revealing previously uncharacterized fragmentation of the diGly scar. Analysis of the LysC-derived ubiquitylated peptides reveal systematic, multidimensional peptide fragmentation, including diagnostic b-ions from fragmentation of the LysC ubiquitin scar. Comprehensively, these findings provide diagnostic spectral signatures of modification events that could applied to new analysis methods for non-tryptic ubiquitylomics.