Mayor T, Graumann J, Bryan J, MacCoss MJ, Deshaies RJ Quantitative profiling of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire influenced by the Rpn10 receptor pathway.
Mol Cell Proteomics. 6(11):1885-95 (2007) 
Tagwerker C, Flick K, Cui M, Guerrero C, Dou Y, Auer B, Baldi P, Huang L, Kaiser P. A tandem affinity tag for two-step purification under fully denaturing conditions: application in ubiquitin profiling and protein complex identification combined with in vivocross-linking.
Mol Cell Proteomics. 5(4):737-48 (2006) 
Seyfried NT, Xu P, Duong DM, Cheng D, Hanfelt J, Peng J. Systematic approach for validating the ubiquitinated proteome.
Anal Chem. 80(11):4161-9 (2008)