Meta-iPep: A Galaxy-based metaimmunopeptidomics bioinformatics pipeline rigorously characterizes microbial peptide antigens bound to the human leukocyte antigen (HLA) complex

Emerging studies have described the presentation of intratumoral microbial peptides by the human leukocyte antigen (HLA) complex. Mass spectrometry (MS)-based metaproteomics can be used to characterize these “metaimmunopeptides,” bettering our understanding of tumor development and progression. However, the complex tumor microbiome presents numerous bioinformatic challenges. The Meta-iPep pipeline was developed on the Galaxy platform to enable bioinformatic analysis of microbial peptides from immunopeptidomic tandem MS (MS/MS) data, allowing researchers to investigate microorganisms that may contribute to cancer.