Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme activation. Mass spectrometry-based proteomics has allowed proteome-scale quantification of hundreds of thousands of ubiquitination sites (ubi-sites). However the regulatory roles and functional importance of most ubi-sites remain undefined. Here, we assembled a human reference ubiquitinome of more than 100,000 ubi-sites by harmonizing public proteomics data.