PCI-DB: a novel primary tissue immunopeptidome database to guide next-generation peptide-based immunotherapy development.

ABSTRACT:

Background

Various cancer immunotherapies rely on the T cell-mediated recognition of peptide antigens presented on human leukocyte antigens (HLA). However, the identification and selection of naturally presented peptide targets for the development of personalized as well as off-the-shelf immunotherapy approaches remain challenging.

Methods

Over 10,000 raw mass spectrometry (MS) files from over 3,000 tissue samples were analyzed, summing to approximately seven terabytes of data. The raw MS data were processed using the standardized and open-source nf-core pipelines MHCquant2 and epitopeprediction, providing a uniform procedure for data handling. A global false discovery rate was applied to minimize false-positive identifications.

Results

Here, we introduce the open-acc

SUBMITTER: Lemke S 

PROVIDER: S-EPMC12001369 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature