Ubiquitination is a posttranslational modification of proteins that involves the 
covalent attachment of ubiquitin, either as a single moiety or as polymers. This 
process controls almost every cellular metabolic pathway through a variety of 
combinations of linkages. Mass spectrometry now allows high throughput 
approaches for the identification of the thousands of ubiquitinated proteins and 
of their ubiquitination sites. Despite major technological improvements in mass 
spectrometry in terms of sensitivity, resolution and acquisition speed, the use 
of efficient purification methods of ubiquitinated proteins prior to mass 
spectrometry analysis is critical to achieve an efficient characterization of 
the ubiquitome. This critical step is achieved using different approaches that 
possess advantages and pitfalls. Here, we discuss the limits that can be 
encountered when deciphering the ubiquitome. This article is part of a Directed 
Issue entitled: Molecular basis of muscle wasting.