⮝ Full datasets listing
PXD058389
PXD058389 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Sensitive direct detection of cancer antigens via user-defined peptide spectral libraries |
| Description | Mass spectrometry (MS) enables precise identification of HLA-bound peptides, but challenges remain in achieving sensitive, accurate, and reproducible detection of rare yet clinically relevant antigens, including predicted tumor neoantigens. Reliable reporting of such rare peptides often requires confirmation with synthetic peptides, which are costly and time-intensive to produce or through prediction of chemical moieties, a strategy that has only recently been expanded to non-tryptic HLA peptides. To generate user-defined high-quality peptide libraries, containing up to 20,000 unique sequences, we introduce Pepyrus, a robust peptide expression system in E. coli. We demonstrate that Pepyrus-generated peptides exhibited close to identical fragmentation patterns, retention times and ion mobility distributions to conventional chemically synthesized peptides. With a HLA-specific data independent acquisition strategy, we recovered >75% of the expected sequences per single injection even at >10,000 peptide Pepyrus library. Pepyrus-assisted identification of rare neoantigens from 0.1 fmol in a complex background was feasible. Personalized Pepyrus libraries facilitated the identification of clinically relevant peptides from melanoma patients, several of which were previously undetected using MS. The customization of Pepyrus allows rapid generation of patient- or disease-specific peptide libraries that enable the confident identification of rare HLA peptides from immunopeptidomics data as well as the generation of large training datasets to improve spectrum, retention time, and ion mobility prediction tools. |
| HostingRepository | MassIVE |
| AnnounceDate | 2025-11-21 |
| AnnouncementXML | Submission_2025-11-21_10:33:42.512.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Claudia Ctortecka |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Acetyl; Oxidation; Carbamidomethyl |
| Instrument | timsTOF Ultra |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-11-28 11:57:02 | ID requested | |
| ⏵ 1 | 2025-11-21 10:33:42 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: immunopeptidomics, DatasetType:Proteomics |
Contact List
| Steven A. Carr | |
|---|---|
| contact affiliation | Broad Institute of MIT and Harvard |
| contact email | scarr@broadinstitute.org |
| lab head | |
| Claudia Ctortecka | |
| contact affiliation | Broad Institute |
| contact email | cctortec@broadinstitute.org |
| 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-ftp.ucsd.edu/v07/MSV000096555/ |
