The immune system has evolved to make repertoires of peptide snapshots processed from self and foreign proteomes, transcriptomes, and genomes, which are displayed in antigen-binding grooves of MHC proteins and scrutinized by T cells. These antigenic peptides are termed Naturally Processed Peptides or Naturally Presented Peptides (NPPs in short), which can be eluted from MHC proteins with weak acid buffer and then purified and identified using HPLC and mass spectrometry. The repertoire and assortment of thousands of peptides displayed by MHC proteins is called immunopeptidome. As the basis of immune recognition of self and non-self, immunopeptidome, either membrane-bound or plasma-soluble, either from a cell or from an allele, either in health or in disease, either natural or virtual, is highly informative. It not only plays an important role in immune tolerance, immune regulation, cell-mediated immunity, transplant rejection, etc.; but also provides valuable information for developing immunodiagnostics, immunotherapeutics, and personalized vaccines. No wonder the immunopeptidome has been described as proteome's mirrors and nature's gene-chips.

We have developed or been developing several tools for mining natural or virtual immunopeptidome data. All of them are hosted in the NIE suite. Among them, P2G is a tool that maps peptidome to proteome, transcriptome, and genome, which is helpful for annotating genomes and finding new genes (see a preliminary demo workflow and its results); iTree produces virtual immunopeptidomes based on proteomes or genomes, calculates their immune distances, and then builds the family tree (intraspecific) or the phylogenetic tree (interspecific); NIEluter predicts CTL epitopes (antigenic peptides) that can be eluted from HLA class I proteins. Go and give it a try!