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PXD040740 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSensitive, high-throughput single-shot HLA-I and HLA-II immunopeptidomics with improved coverage using data dependent parallel accumulation-serial fragmentation mass spectrometry
DescriptionPhulphagar 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.
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterKarl Clauser
SpeciesList scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationListunknown modification; unknown modification
InstrumentOrbitrap Exploris 480; timsTOF SCP
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-03-09 16:43:19ID requested
12023-05-25 10:24:05announced
Publication List
no publication
Keyword List
submitter keyword: immunopeptidomics, timsTOF
Contact List
Steven A. Carr
contact affiliationBroad Institute of MIT and Harvard
contact emailscarr@broadinstitute.org
lab head
Karl Clauser
contact affiliationBroad Institute of MIT and Harvard
contact emailclauser@broadinstitute.org
dataset submitter
Full Dataset Link List
MassIVE dataset URI
Dataset FTP location
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