PXD008733

PXD008733 is an original dataset announced via ProteomeXchange.

Title	A tissue-based draft map of the murine MHC class I immunopeptidome
Description	The array of peptides presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules is referred to as the MHC class I immunopeptidome. Although the MHC class I immunopeptidome is ubiquitous in mammals and represents a critical component of the adaptive immune system, very little is known about its baseline composition across all tissues and organs in vivo. In this study, we applied mass spectrometry (MS) technologies to draft a tissue-based atlas of the MHC class I immunopeptidome in the C56BL/6 mouse model. Overall, 19 normal mouse tissues were extracted and a total number of ~30,000 high-confidence H2Db/Kb-associated peptides were identified and annotated in the atlas. The raw MS output files, the catalogue of H2Db/Kb-associated peptides, the tissue origin(s) of individual peptides and the H2Db/Kb-specific peptide spectral libraries, which consist of consensus spectra calculated from repeat measurements of the same peptide sequence, were shared via the SysteMHC Atlas project (dataset identifier SYSMHC00018). We expect that this unique dataset will be further expended in the future and will be re-used by the community to 1) investigate the tissue-specificity of the immunopeptidome, 2) perform highly reproducible spectral library-based analysis of immunopeptidomes from mice cohorts, and 3) rapidly identify disease-specific H2Db/Kb peptide antigens from various mouse models of autoimmune diseases and cancers.
HostingRepository	PRIDE
AnnounceDate	2018-06-19
AnnouncementXML	Submission_2018-08-27_07:36:25.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Etienne Caron
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue
Instrument	Orbitrap Fusion Lumos; TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2018-01-22 01:48:29	ID requested
1	2018-06-19 00:57:21	announced
⏵ 2	2018-08-27 07:36:26	announced	Updated publication reference for PubMed record(s): 30084848.

Schuster H, Shao W, Weiss T, Pedrioli PGA, Roth P, Weller M, Campbell DS, Deutsch EW, Moritz RL, Planz O, Rammensee HG, Aebersold R, Caron E, A tissue-based draft map of the murine MHC class I immunopeptidome. Sci Data, 5():180157(2018) [pubmed]

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

curator keyword: Biological

submitter keyword: MHC, immunopeptidome, mass spectrometry, tissue, map

Ruedi Aebersold
contact affiliation	Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, 8093, Switzerland
contact email	aebersold@imsb.biol.ethz.ch
lab head
Etienne Caron
contact affiliation	ETH Zurich
contact email	caron@imsb.biol.ethz.ch
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/2018/06/PXD008733

PRIDE project URI

• PRIDE
  1. PXD008733
     1. Label: PRIDE project
     2. Name: A tissue-based draft map of the murine MHC class I immunopeptidome