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PXD008151

PXD008151 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleAnalysis of bovine leukocyte antigen (BoLA)-associated peptides by LC-MS
DescriptionAn increasing amount of MHC presented peptides identified by mass spectrometry (MS ligands) has been published. Handling and interpretation of MS ligand data is in general challenging due to the poly-specificity nature of the data. We here outline a general pipeline for dealing with this challenge, and accurately annotate ligands to the relevant MHC-I molecule they were eluted from by use of GibbsClustering and binding motif information inferred from in-silico models. We illustrate the approach here in the context of MHCI molecules (BoLA) of cattle. Next, we demonstrate how such annotated BoLA MS ligand data can readily be integrated with in-vitro binding affinity data in a prediction model with very high and unprecedented performance for identification of BoLA-I restricted T cell epitopes.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_04:41:57.340.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterNicola Ternette
SpeciesList scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02017-11-07 02:25:15ID requested
12017-11-20 05:57:45announced
22019-01-03 02:27:53announcedUpdated publication reference for PubMed record(s): 30578603, 29115832.
32024-10-22 04:42:07announced2024-10-22: Updated project metadata.
Publication List
10.1021/acs.jproteome.7b00675;
Andreatta M, Nicastri A, Peng X, Hancock G, Dorrell L, Ternette N, Nielsen M, MS-Rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments. Proteomics, 19(4):e1800357(2019) [pubmed]
10.1002/pmic.201800357;
Nielsen M, Connelley T, Ternette N, Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data. J Proteome Res, 17(1):559-567(2018) [pubmed]
Keyword List
ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP)
curator keyword: Biological
submitter keyword: immunopeptidomics,BoLA
Contact List
Nicola Ternette
contact affiliationUniversity of Oxford, Target Discovery Institute Mass Spectrometry Laboratory The Jenner Insitute
contact emailnicola.ternette@ndm.ox.ac.uk
lab head
Nicola Ternette
contact affiliationUniversity of Oxford
contact emailnicola.ternette@ndm.ox.ac.uk
dataset submitter
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Dataset FTP location
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PRIDE project URI
Repository Record List
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