Mass spectrometry‑based identification of peptides presented by major histocompatibility complex in macrophages

Immunopeptidomics is a field of research that has progressed in thelast years due to advances in sophisticated analytical techniquesbased on mass spectrometry and bioinformatics. The ability to identifymolecules to the extent of a single ion led to a step forward inimmunopeptidomics. Mass spectrometry enables the identificationof thousands of peptide sequences in a single sample, thus providinglarge-scale reliable information. The immunopeptidome is the entire group of peptides presented by the major histocompatibility complexClass-I (MHC-I), at the surface of all nucleated cells and Class II, at thesurface of professional antigen presenting cells. The MHC-bound peptidesare recognized by T cells and constitute the immunological synapse,leading to the initiation of the adaptive immune response. Underpathological conditions, peptides originating from the proteolysis ofpathogen proteins are presented to the cells of the host immune systemvia MHC. Thus, the identification of pathogen peptides throughimmunopeptidomics is an unbiased method for understanding thegeneration of adaptive immune responses against pathogens.Here we describe the establishment of a new mass spectrometrybasedimmunopeptidomics platform for peptide identification inphysiological and pathological conditions. Using the macrophage cellline with THP-1, with a known HLA-type, we were able to identify atotal of 2913 unique MHC-I bound peptides. The peptide length distribution,NetMHCpan-4.1 rank affinity, and best match HLA bindingallele for each peptide will be presented.Finally, identifying MHC-I and MHC-II peptides under physiologicaland pathological conditions could uncover the most relevant peptidesable to stimulate the right type of T-cell response for vaccine designand development.