PXD027859

PXD027859 is an original dataset announced via ProteomeXchange.

Title	B27 inmunopeptidome in vaccinica infected cells
Description	Identification of natural human leukocyte antigen (HLA) ligandome is a key element to understand the cellular immune responses. Advanced high throughput mass spectrometry analyses identify a relevant, but not complete, fraction of the many tens of thousands of self-peptides generated by the antigen processing in live cells. In infected cells, in addition to this complex HLA ligandome, a minority of peptides from degradation of the few proteins encoded by the viral genome are also bound to HLA class I molecules. In this study, the standard immunoproteomics strategy was modified to include the classical acid stripping treatment after virus infection to enrich the HLA ligandome in virus ligands. Complexes of HLA-B*27:05-bound peptide pools were isolated from vaccinia virus (VACV)-infected cells treated with acid stripping after virus infection. The HLA class I ligandome was identified using high throughput mass spectrometry analyses, yielding 42 and 52 natural peptides processed and presented in untreated and after acid stripping treatment VACV-infected human cells, respectively. Most of these virus ligands were identified in both conditions, but a relevant fraction of VACV ligands detected by mass spectrometry was dependent of acid stripping treatment with almost twice more exclusive viral ligands that the untreated VACV-infected condition. Theoretical binding affinity prediction of the VACV HLA-B*27:05 ligands and acute antiviral T cell response characterization in the HLA transgenic mice model showed no differences between HLA ligands identified under the two conditions: untreated and acid stripping condition. These findings indicated that acid stripping treatment could be useful to identify HLA class I ligands from virus-infected cells.
HostingRepository	PRIDE
AnnounceDate	2021-12-22
AnnouncementXML	Submission_2021-12-22_02:51:41.787.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Miguel Marcilla
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-11 04:27:33	ID requested
⏵ 1	2021-12-22 02:51:42	announced

Lorente E, Marcilla M, de la Sota PG, Quijada-Freire A, Mir C, L, ó, pez D, Acid Stripping after Infection Improves the Detection of Viral HLA Class I Natural Ligands Identified by Mass Spectrometry. Int J Mol Sci, 22(19):(2021) [pubmed]

submitter keyword: HLA, HLA-B*27, Vaccinica, Immunopeptidomics

Fernando Corrales
contact affiliation	Proteomics Unit and Functional Proteomics Group. Spanish National Biotechnology Centre (CNB-CSIC).
contact email	fcorrales@cnb.csic.es
lab head
Miguel Marcilla
contact affiliation	Proteomics Unit - Dpt. of Macromolecular Structures - Spanish National Biotechnolgy Centre (CNB-CSIC)
contact email	mmarcilla@cnb.csic.es
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD027859
     1. Label: PRIDE project
     2. Name: B27 inmunopeptidome in vaccinica infected cells