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. 2023 May 3;22(6):100563. doi: 10.1016/j.mcpro.2023.100563

Fig. 5.

Fig. 5

Single-shot DDA-PASEF of low-input primary melanoma tumors on the timsTOF single-cell proteomics (SCP) enables deep profiling of the HLA-I immunopeptidome and detection of cancer-testis antigen (CTA) and novel unannotated ORF (nuORF)–derived peptides.A, unique HLA-I peptides enriched from 15 mg wet weight primary melanoma tumors (estimated <1e7 cells) identified by single-shot injections on timsTOF SCP with methods M10–M11. B, peptides detected in A that map CTA source proteins from CTdatabase (44). C, unique nuORF source proteins represented in HLA-I immunopeptidome of the respective melanoma tumors (6). D, quality metrics of HLA-I peptides from primary melanoma tumors including median score, %SPI, BCS, median PDI, and scores by charge state using M10 or M11 on the SCP. %SPI, percent scored peak intensity; BCS, backbone cleavage score; DDA, data-dependent acquisition; HLA, human leukocyte antigen; PASEF, parallel accumulation-serial fragmentation; PDI, percent precursor dissociation intensity.