Linkage specific poly-ubiquitin chains are used to investigate mechanisms of chain recognition, binding and hydrolysis by the proteasome, deubiquitinating enzymes, E3 ligases or other proteins that contain ubiquitin-associated domains (UBAs) or ubiquitin-interacting motifs (UIMs). Lys48- linked chains are abundant in vivo and act as a universal signal for proteasomal degradation. This product is formed with wild-type human recombinant ubiquitin and linkage-specific enzymes. This mixture of poly-ubiquitin chains contains di-ubiquitin and higher MW species; monoubiquitin has been removed.