PXD053374-1
PXD053374 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | diaPASEF for HLA-I peptide analysis enables quantification of common cancer neoantigens |
| Description | Human leukocyte antigen class I (HLA-I) molecules present short peptide sequences from endogenous or foreign proteins to cytotoxic T cells. Low abundance of HLA-I peptides poses significant technical challenges for their identification and accurate quantification. While mass spectrometry (MS) is currently a method of choice for direct system-wide identification of cellular immunopeptidome, there is still a need for enhanced sensitivity in detecting and quantifying tumor specific epitopes. As gas phase separation in data dependent MS data acquisition (DDA) increased HLA-I peptide detection by up to 50%, here, we aimed to evaluate the performance of data independent acquisition (DIA) in combination with ion mobility (diaPASEF) for high sensitivity identification of HLA presented peptides. Our streamlined diaPASEF workflow enabled identification of 11,412 unique peptides from 12.5 million A375 cells and 3,426 8-11mers from as low as 500,000 cells with high reproducibility. By taking advantage of HLA binder-specific in-silico predicted spectral libraries, we were able to further increase the number of identified HLA-I peptides. We applied SILAC-DIA to a mixture of labeled HLA-I peptides, calculated heavy to light ratios for 7,742 peptides across 5 conditions and demonstrated that diaPASEF achieves high quantitative accuracy up to 4-fold dilution. Finally, we identified and quantified shared neoantigens in a monoallelic C1R cell line model. By spiking in heavy synthetic peptides, we verified identification of the peptide sequence and calculated relative abundances for 13 neoantigens. Taken together, diaPASEF analysis workflows for HLA-I peptides can increase the peptidome coverage for lower sample amounts. The sensitivity and quantitative accuracy provided by DIA can enable the detection and quantification of less abundant peptide species such as neoantigens across samples from the same background. |
| HostingRepository | MassIVE |
| AnnounceDate | 2025-03-11 |
| AnnouncementXML | Submission_2025-03-11_14:49:07.155.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Susan Klaeger |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Oxidation; Cysteinyl; Carbamidomethyl |
| Instrument | timsTOF SCP |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-06-24 14:41:37 | ID requested | |
| ⏵ 1 | 2025-03-11 14:49:07 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: immunopeptidomics, DIA, HLA, MHC |
Contact List
| Susan Klaeger | |
|---|---|
| contact affiliation | Genentech, Inc. |
| contact email | klaeger.susan@gene.com |
| lab head | |
| Susan Klaeger | |
| contact affiliation | Genentech |
| contact email | klaeger.susan@gene.com |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/v08/MSV000095137/ |
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