PXD008151

PXD008151 is an original dataset announced via ProteomeXchange.

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

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.

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]

ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP)

curator keyword: Biological

submitter keyword: immunopeptidomics,BoLA

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

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.pride.ebi.ac.uk/pride/data/archive/2017/11/PXD008151

PRIDE project URI

• PRIDE
  1. PXD008151
     1. Label: PRIDE project
     2. Name: Analysis of bovine leukocyte antigen (BoLA)-associated peptides by LC-MS