HLA Ligand Atlas DIA: extending the benign immunopeptidomics resource with increased sensitivity through...

Area of Science:

• Immunology
• Proteomics
• Mass Spectrometry

Background:

• The human leukocyte antigen (HLA)-presented peptide repertoire, or immunopeptidome, is vital for T-cell immunity.
• The HLA Ligand Atlas previously mapped the immunopeptidome of non-malignant tissues using data-dependent acquisition (DDA) mass spectrometry.
• This resource serves as a reference for antigen discovery, particularly in cancer immunotherapy.

Purpose of the Study:

• To expand the HLA Ligand Atlas with paired data-independent acquisition (DIA) mass spectrometry data.
• To enhance the depth and range of analyses possible with the HLA Ligand Atlas dataset.
• To showcase the advantages of DIA over DDA for immunopeptidomic studies.

Main Methods:

• Generated 946 DIA HLA class I and II immunopeptidomic runs from 242 non-malignant human samples across 18 subjects and 29 tissues.
• Integrated novel DIA data with existing DDA data from the HLA Ligand Atlas.
• Performed an HLA-A*02:01 allotype-specific spectral library search to demonstrate superior sensitivity.

Main Results:

• The new dataset significantly extends the range and depth of analyses for the HLA Ligand Atlas.
• DIA mass spectrometry offers advantages over DDA in spectral sampling and sensitivity due to increased dynamic range.
• Low signal intensity peptide transitions were identified more effectively using DIA.

Conclusions:

• The expanded HLA Ligand Atlas, incorporating DIA data, provides a more comprehensive resource for human immunology.
• DIA mass spectrometry enhances the identification and quantification of HLA-presented peptides.
• Researchers are encouraged to reanalyze the combined DDA and DIA data for future immunological studies.