Before we advance further on the discussion of isopeptide products generated from target proteins that have been ubiquitinated or SUMOylated, it is important to simplify their terminology:
1) In the literature, isopeptides are commonly also referred to as ubiquitin peptides, ubiquitinated peptides, ubiquitinated isopeptides, SUMO peptides, SUMOylated peptides, and SUMOylated isopeptides. However, in order to simplify things, the isopeptide products that are generated from target proteins that have been ubiquitinated are referred to as Ub-isopeptides. Isopeptide products that have been generated from target proteins that have been SUMOylated are referred to as follows: (i) SUMO(x)-isopeptides, with “x” referring to the specific type of SUMOylation PTM that the isopeptide has been derived from SUMO(1), SUMO(2), or SUMO(3), or (ii) SUMO-isopeptides when generalizing.
2) The truncated version of the Ub/Ubl modification that is covalently attached to the peptide backbone of the isopeptide via the isopeptide bond postdigestion is commonly referred to in literature as a remnant, a branch, an iso-tag, or an iso-chain. However, in order to simplify things, this is referred to in this chapter as an iso-chain.