Fig. 1.

Overview of the application of DIA immunopeptidomics. A schematic overview of the application of sample-specific library for DIA approach for immunopeptidomics (A) and multi-HLA library for DIA immunopeptidomics leveraging existing large-scale immunopeptidomics datasets (B). As a proof of concept, we applied the MaxQuant and Spectronaut computational environments for DDA library preparation and DIA data analysis, respectively. Schematic representation of the variable isolation windows across the m/z space applied for the DIA acquisition method (C). Histogram of m/z values of all HLA peptides included in the multi-HLA BigLib spectral library (D). DDA, data-dependent MS/MS acquisition; DIA, data-independent acquisition; HLA, human leukocyte antigen.