Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome.

ABSTRACT: Spliced peptides are short protein fragments spliced together in the proteasome by peptide bond formation. True estimation of the contribution of proteasome-spliced peptides (PSPs) to the global human leukocyte antigen (HLA) ligandome is critical. A recent study suggested that PSPs contribute up to 30% of the HLA ligandome. We performed a thorough reanalysis of the reported results using multiple computational tools and various validation steps and concluded that only a fraction of the proposed PSPs passes the quality filters. To better estimate the actual number of PSPs, we present an alternative workflow. We performed de novo sequencing of the HLA-peptide spectra and discarded all de novo sequences found in the UniProt database. We checked whether the remaining de novo</

SUBMITTER: Mylonas R 

PROVIDER: S-EPMC6283289 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature