Beyond HCD: complementary fragmentation chemistries expand HLA class I immunopeptidome discovery
Terry C.C. Lim Kam Sian, Fernanda Salvato, Nivedhitha Selvakumar, Tima Shamekhi, Josh Hinkle, Christopher Mullen, Gabriel A Goncalves, Ralf B. Schittenhelm, Pouya Faridi
This paper evaluates CID and IRMPD fragmentation methods for HLA class I immunopeptidomics, finding they identify unique peptides missed by HCD, especially for non-basic anchor alleles and peptides lacking lysine, arginine, or histidine.
bioRxiv · Sep 30, 2026 · PreprintImmunology