PXD043844
PXD043844 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in TimsTOF |
| Description | Immunopeptidomics plays a crucial role in identifying targets for immunotherapy and vaccine development. Because the generation of immunopeptides from their parent proteins does not adhere to clear-cut rules, rather than being able to use known digestion patterns, every possible protein subsequence within HLA class-specific length restrictions needs to be considered. This leads to an inflation of the search space and results in lower spectrum annotation rates. Rescoring is a powerful enhancement of standard sequence database searching that boosts the spectrum annotation performance. In the field of immunopeptidomics low abundant peptides often occur, which is why the highly sensitive timsTOF instruments are increasingly gaining popularity. To improve rescoring for immunopeptides measured using timsTOF instruments, we trained a deep learning-based fragment ion intensity prediction model. Over 300,000 synthesized non-tryptic peptides from the ProteomeTools project were analyzed on a timsTOF-Pro to generate a dataset that was used to fine-tune an existing Prosit model. By applying our fragment ion intensity prediction model, we demonstrate up to 3-fold improvement in the identification of immunopeptides. Furthermore, our approach increased detection of immunopeptides even from low input samples. |
| HostingRepository | MassIVE |
| AnnounceDate | 2023-07-17 |
| AnnouncementXML | Submission_2023-07-17_09:02:40.996.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Charlotte Adams |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | unknown modification; unknown modification |
| Instrument | timsTOF Pro |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2023-07-17 08:19:25 | ID requested | |
| ⏵ 1 | 2023-07-17 09:02:41 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: timsTOF, Prosit, immunopeptidomics |
Contact List
| Wout Bittremieux | |
|---|---|
| contact affiliation | University of Antwerp |
| contact email | wout.bittremieux@uantwerpen.be |
| lab head | |
| Kurt Boonen | |
| contact affiliation | University of Antwerp |
| contact email | kurt.boonen@uantwerpen.be |
| lab head | |
| Charlotte Adams | |
| contact affiliation | University of Antwerp |
| contact email | charlotte.adams@uantwerpen.be |
| 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/MSV000092456/ |
to receive all new ProteomeXchange dataset release announcements!
