PXD039353

PXD039353 is an original dataset announced via ProteomeXchange.

Title	Large-scale profiling of unexpected tryptic cleaved sites at ubiquitinated lysines
Description	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.
HostingRepository	iProX
AnnounceDate	2023-01-10
AnnouncementXML	Submission_2023-12-21_20:18:43.834.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhen Sun
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	ubiquitination signature dipeptidyl lysine
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-10 18:55:57	ID requested
1	2023-01-10 18:56:15	announced
⏵ 2	2023-12-21 20:18:44	announced	2023-12-22: Update publication information.

Sun Z, Xiao W, Li N, Chang L, Xu P, Li Y, Large-Scale Profiling of Unexpected Tryptic Cleaved Sites at Ubiquitinated Lysines. J Proteome Res, 22(4):1245-1254(2023) [pubmed]

submitter keyword: trypsin, exopeptidase activity, irregular cleavage, ubiquitination

Ping Xu
contact affiliation	Beijing Proteome Research Center
contact email	xuping_bprc@126.com
lab head
Zhen Sun
contact affiliation	Beijing Proteome Research Center
contact email	sunzhen1710@foxmail.com
dataset submitter

iProX dataset URI