A Platform for High-throughput and Ultrasensitive Immunopeptidomics

Mass spectrometry-based immunopeptidomics is a powerful approach for untargeted discovery of peptides presented on MHC molecules, which can guide the selection of vaccine antigens and immunotherapy targets. First-generation immunopeptidomics workflows require processing of hundreds of millions of cells using lengthy, manual procedures. More recent approaches focus on increasing either sensitivity or throughput, but rarely combine both aspects. Here, we describe a semiautomated immunopeptidomics platform that combines high sensitivity with high throughput by implementing highly optimized conditions for isolation of MHC class I and II peptides in a 96-well positive pressure device. Lysis in a small volume of 100 μl allows efficient MHC capture in a 96-well filter plate with optimal pore size for automated washing, elution, and C18 purification steps. Upon analysis of 25% of the eluate from 16 million cells, our workflow identified over 13,500 MHC I and 6000 MHC II peptides on a timsTOF single-cell proteomics mass spectrometer, operating in data-dependent acquisition-parallel accumulation-serial fragmentation mode. Exploring the sensitivity limits of our platform, we identified up to 1000 MHC I peptides, including hundreds of predicted binders, from as few as 20,000 JY cells. Validating the platform's performance for quantitative biological discovery, we report the identification of known and novel bacterial immunopeptides from U937 macrophages infected with Listeria monocytogenes or bacillus Calmette-Guérin. Together, our optimized immunopeptidomics platform enables robust immunopeptide detection from lower-input samples in a high-throughput fashion, enabling its use for biological applications where sample amounts are limiting.