Fig. 1.

diaPASEF identifies HLA peptides with high reproducibility.A, overview of HLA peptide enrichment workflow. B, a sample-specific spectral library was created from HLA peptides eluted from 3x 25 e6 cells, fractionated and acquired in ddaPASEF mode. Four replicates were analyzed in diaPASEF mode, and spectra were interpreted using DIA-NN with the sample matched spectral library. C, number of unique peptide identifications. D, length distribution of peptide IDs. E, charge distribution. F, intensity correlation between two replicates. G, fraction of observed peptides assigned to alleles in DDA library and DIA peptide identifications. DDA, data-dependent acquisition; DIA, data-independent acquisition; HLA, human leukocyte antigen.