Chemical Derivatization Strategy for Extending the Identification of MHC Class I Immunopeptides

Area of Science:

• Immunology
• Analytical Chemistry
• Oncology

Background:

• Neoantigen-based vaccines hold promise for cancer treatment by targeting tumor-specific antigens.
• Mass spectrometry (MS)-based immunopeptidomics is vital for identifying these tumor-associated epitopes and neoantigens.
• Challenges remain in detecting low-abundance peptides and improving MS/MS identification rates for major histocompatibility complex (MHC) peptides.

Purpose of the Study:

• To develop and apply a novel chemical derivatization strategy to enhance the coverage of the MHC peptidome.
• To improve the identification of low-abundance and mutation-bearing peptides for neoantigen discovery.

Main Methods:

• A novel chemical derivatization strategy was developed, combining analysis of native, dimethylated, and alkylamidated peptides.
• Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was employed to analyze the derivatized peptides.
• The strategy focused on improving hydrophobicity, ionization efficiency, and MS/MS fragmentation of MHC peptides.

Main Results:

• Dimethylation increased hydrophobicity and ionization efficiency of MHC class I peptides.
• Alkylamidation significantly improved MS/MS fragmentation, leading to a higher yield of y-ions.
• The combined strategy identified 3148 unique MHC I peptides from HCT 116 cell lines, a substantial increase from 1388 native peptides, including 10 high-confidence mutation-bearing peptides.

Conclusions:

• The developed chemical derivatization strategy effectively expands the coverage of the MHC peptidome.
• This approach significantly enhances the identification of MHC peptides, including mutation-bearing neoantigens.
• The strategy shows great promise for advancing neoantigen discovery in clinical cancer vaccine applications.