Utilizing Protein Bioinformatics to Delve Deeper Into Immunopeptidomic Datasets

Immunopeptidomics is a growing subfield of proteomics that has the potential to shed new light on a long-neglected aspect of adaptive immunology: a comprehensive understanding of the peptides presented by major histocompatibility complexes (MHC) to T cells. As the field of immunopeptidomics continues to grow and mature, a parallel expansion in the methods for extracting quantitative features of these peptides is necessary. Currently, massive experimental efforts to isolate a given immunopeptidome are summarized in tables and pie charts, or worse, entirely thrown out in favor of singular peptides of interest. Ideally, an unbiased approach would dive deeper into these large proteomic datasets, identifying sequence-level biochemical signatures inherent to each individual dataset and the given immunological niche. This chapter will outline the steps for a powerful approach to such analysis, utilizing the Automated Immune Molecule Separator (AIMS) software for the characterization of immunopeptidomic datasets. AIMS is a flexible tool for the identification of biophysical signatures in peptidomic datasets, the elucidation of nuanced differences in repertoires collected across tissues or experimental conditions, and the generation of machine learning models for future applications to classification problems. In learning to use AIMS, readers of this chapter will receive a broad introduction to the field of protein bioinformatics and its utility in the analysis of immunopeptidomic datasets and other large-scale immune repertoire datasets.