Biologically informed benchmarking reveals complementary computational strategies for non-reference HLA-presented peptide discovery

This dataset accompanies our study on benchmarking computational strategies for the discovery of non-reference HLA-presented peptides in immunopeptidomics. The primary goal of this repository is to ensure reproducibility and transparency by providing all data and code necessary to reproduce the key figures and analyses presented in the manuscript. In addition, the dataset includes detailed annotations to facilitate interpretation and reuse.