MassIVE MSV000091456

Partial Public PXD040740

Sensitive, high-throughput single-shot HLA-I and HLA-II immunopeptidomics with improved coverage using data dependent parallel accumulation-serial fragmentation mass spectrometry

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Description

Phulphagar K, Ctortecka C, Vaca Jacome AS, Klaeger S, Verzani E, Hernandez G, Udeshi ND, Clauser KR, Abelin JG, Carr SA. 2023. Comprehensive, in-depth identification of the human leukocyte antigen HLA-I and HLA-II tumor immunopeptidome can inform the development of cancer immunotherapies. Mass spectrometry (MS) is a powerful state-of-the-art technology for direct identification of HLA peptides from patient derived tumor samples or cell lines. However, achieving sufficient coverage to detect rare, clinically relevant antigens requires highly sensitive MS-based acquisition methods and large amounts of samples. Immunopeptidome depth can be increased through biochemical fractionation, which can be impeded by the limited amounts of primary tissue biopsies. To address this challenge, we developed and applied a high throughput, sensitive, single-shot MS-based immunopeptidomics workflow that leverages trapped ion mobility time-of-flight mass spectrometry on the Bruker timsTOF SCP. We demonstrate >2-fold improved coverage of HLA immunopeptidomes with up to 15,000 distinct HLA-I and HLA-II peptides from 4e7 cells. Our optimized single-shot MS acquisition method on the SCP maintains high coverage, eliminates the need for biochemical fractionation and reduces input requirements to 1e7 cells for > 800 distinct HLA-I peptides. Moreover, we find that the binding motifs of specific HLA alleles can influence peptide fragmentation patterns, and that optimized collision energies can result in complementary b/y ion sequence coverage. Our optimized single-shot SCP acquisition methods enable sensitive, high throughput and reproducible immunopeptidome profiling and the detection of peptides from non-canonical open reading frames and clinically relevant cancer-testis antigens from less than 4e7 cells or 15 mg wet weight tissue. [doi:10.25345/C5DF6KD0D] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: immunopeptidomics ; timsTOF

Contact

Principal Investigators:
(in alphabetical order) 		Steven A. Carr, Broad Institute of MIT and Harvard, United States
Submitting User: clauser
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