Large-scale profiling of unexpected tryptic cleaved sites at ubiquitinated lysines

ABSTRACT: Trypsin specifically cleaves the C-terminus of lysine and arginine residues and is assumed to fails to cleave ubiquitin-modified sites. Based on this perception, the irregularly-cleaved ubiquitinated peptides were often regarded as false positives and discarded in proteomic analysis. Interestingly, unexpected cleavage at the modified ubiquitin K48 site has been reported, suggesting the latent ability of trypsin to cleave the C-terminus of modified lysines. However, it remains unclear whether other trypsin-cleavable ubiquitinated sites are present. In this study, we verified the ability of trypsin in cleaving K6 and K63 besides K48 chains. The missed cleaved K-ε-GG peptide was quickly and efficiently generated during trypsin digestion, whereas irregularly-cleaved ones were produced more slowly and with much lower efficiency. To confirm the availability of K-ε-GG antibody purified ubiquitinome datasets, the K-ε-GG antibody was proved to efficiently enrich the irregularly-cleaved peptides. More than 3,000 irregularly-cleaved ubiquitylated peptides were identified in the K-ε-GG antibody and UbiSite based datasets, and the frequency of lysine upstream of the irregularly-cleaved modified K was significantly enriched. The kinetic activity of trypsin in cleaving modified lysine residues was further elucidated. We suggest that irregularly-cleaved K-ε-GG sites with high identification scores should be considered as true positives in future ubiquitome analyses.

ORGANISM(S): Homo Sapiens

SUBMITTER: Ping Xu  

PROVIDER: PXD039353 | iProX | Tue Jan 10 00:00:00 GMT 2023

REPOSITORIES: iProX