Extended Data Fig. 5: Signature MS2 ions of 2xGG-Ub(1-74) species.
From: cIAP1-based degraders induce degradation via branched ubiquitin architectures
a. Schematic representation of the Ub(1–74) species modified with two di-Gly remnants (2xGG Ub) and the corresponding masses of the y ions. Because K11-, K48-, and K63-linkages account for ~95% of the total ubiquitin chains, most of the 2xGG Ubs are modified at either K11/K48, K11/K63, or K48/K63. When the 2xGG Ub peptides are fragmented using higher collision energy dissociation (HCD), the y38 and y12 ions have different masses depending on the sites where the GGs are conjugated. Specifically, the y38 ion containing two GGs represents the signature for K48/K63 branched linkages. Likewise, the y12 ion that contains no GGs represents the signature for K11/K48 branched linkages.
