PXD008151 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Analysis of bovine leukocyte antigen (BoLA)-associated peptides by LC-MS |
Description | An 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. |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_04:41:57.340.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Nicola Ternette |
SpeciesList | scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2017-11-07 02:25:15 | ID requested | |
1 | 2017-11-20 05:57:45 | announced | |
2 | 2019-01-03 02:27:53 | announced | Updated publication reference for PubMed record(s): 30578603, 29115832. |
⏵ 3 | 2024-10-22 04:42:07 | announced | 2024-10-22: 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 affiliation | University of Oxford, Target Discovery Institute Mass Spectrometry Laboratory The Jenner Insitute |
contact email | nicola.ternette@ndm.ox.ac.uk |
lab head | |
Nicola Ternette |
contact affiliation | University of Oxford |
contact email | nicola.ternette@ndm.ox.ac.uk |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD008151
- Label: PRIDE project
- Name: Analysis of bovine leukocyte antigen (BoLA)-associated peptides by LC-MS