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PXD043844

PXD043844 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleFragment ion intensity prediction improves the identification rate of non-tryptic peptides in TimsTOF
DescriptionImmunopeptidomics 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.
HostingRepositoryMassIVE
AnnounceDate2023-07-17
AnnouncementXMLSubmission_2023-07-17_09:02:40.996.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterCharlotte Adams
SpeciesList scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationListunknown modification; unknown modification
InstrumenttimsTOF Pro
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-07-17 08:19:25ID requested
12023-07-17 09:02:41announced
Publication List
no publication
Keyword List
submitter keyword: timsTOF, Prosit, immunopeptidomics
Contact List
Wout Bittremieux
contact affiliationUniversity of Antwerp
contact emailwout.bittremieux@uantwerpen.be
lab head
Kurt Boonen
contact affiliationUniversity of Antwerp
contact emailkurt.boonen@uantwerpen.be
lab head
Charlotte Adams
contact affiliationUniversity of Antwerp
contact emailcharlotte.adams@uantwerpen.be
dataset submitter
Full Dataset Link List
MassIVE dataset URI
Dataset FTP location
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