PXD040385

PXD040385 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with novel MS2PIP timsTOF fragmentation prediction model
Description	Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, and patient individuality. Here, we developed a highly sensitive method for identifying HLAIps using liquid chromatography-ion mobility-tandem mass spectrometry (LC-IMS-MS/MS). In addition, we trained a novel timsTOF-specific peak intensity MS2PIP model for tryptic and non-tryptic peptides and implemented it in MS2Rescore (v3) together with the CCS predictor from ionmob. The optimized method, Thunder-DDA-PASEF, semi-selectively fragments singly and multiply charged HLAIps based on their IMS and m/z. Moreover, the method employs the high sensitivity mode and extended IMS resolution with fewer MS/MS frames (300 ms TIMS ramp, 3 MS/MS frames), doubling the coverage of immunopeptidomics analyses, compared to the proteomics-tailored DDA-PASEF (100 ms TIMS ramp, 10 MS/MS frames). Additionally, rescoring boosted the HLAIps identification by 41.7% to 33%. This enabled in-depth profiling of HLAIps from diverse human cell lines and human plasma. Finally, profiling JY and Raji cells transfected to express the SARS-CoV-2 spike protein resulted in 16 spike HLAIps, thirteen of which had been reported to elicit immune responses in human patients.
HostingRepository	jPOST
AnnounceDate	2024-03-18
AnnouncementXML	Submission_2024-03-17_08:00:14.434.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	David Gomez-Zepeda
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	unknown modification; alpha-amino acetylated residue; L-methionine sulfoxide; unknown modification; S-carboxamidomethyl-L-cysteine
Instrument	instrument; Orbitrap Exploris 480

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-24 05:13:44	ID requested
⏵ 1	2024-03-17 08:00:15	announced

Publication List

Gomez-Zepeda D, Arnold-Schild D, Beyrle J, Declercq A, Gabriels R, Kumm E, Preikschat A, Ł, ą, cki MK, Hirschler A, Rijal JB, Carapito C, Martens L, Distler U, Schild H, Tenzer S, PIP timsTOF fragmentation prediction model. Nat Commun, 15(1):2288(2024) [pubmed]

Gomez-Zepeda D, Arnold-Schild D, Beyrle J, Declercq A, Gabriels R, Kumm E, Preikschat A, Ł, ą, cki MK, Hirschler A, Rijal JB, Carapito C, Martens L, Distler U, Schild H, Tenzer S, PIP timsTOF fragmentation prediction model. Nat Commun, 15(1):2288(2024) [pubmed]

Keyword List

submitter keyword: DDA-PASEF, SARS-CoV-2 spike protein, HLAIp, immunopeptidomics, timsTOF

submitter keyword: DDA-PASEF, SARS-CoV-2 spike protein, HLAIp, immunopeptidomics, timsTOF

Contact List

Prof. Dr. Stefan Tenzer
lab head
David Gomez-Zepeda
contact affiliation	HI-TRON, DKFZ
dataset submitter

Full Dataset Link List

jPOST dataset URI
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jPOST 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://ftp.jpostdb.org/JPST002044/