PXD034788

PXD034788 is an original dataset announced via ProteomeXchange.

Title	Large-Scale Immuno-Peptidome Analysis Reveals Recurrent Post-Translational Splicing of Cancer and Immune-Associated Genes
Description	Post translational spliced peptides bound to the HLA are unique type of peptides, shown in cancer, for HLA-class-I. Thus far, no consensus has been reached on the extent to which post-translational spliced peptides (PTSPs) occur, stirring significant debate. Furthermore, the role of the HLA-class-II pathway has been studied only in diabetes. Here, we exploit our large-scale cancer peptidomics database and devise a pipeline to filter spliced peptide predictions, to identify recurring spliced peptides, both for HLA-class-I and -II. Our results indicate that HLA-Class-I spliced peptides account for a low percentage (4.4%) of the immunopeptidome, yet are larger in number relative to other types of identified aberrant peptides. Therefore, spliced peptides contribute significantly to the repertoire of presented peptides in cancer cells. In addition, HLA-class-II bound spliced peptides were identified as well, but to a lower extent (0.6%).
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:47:36.148.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ronen Levy
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-21 07:21:58	ID requested
1	2023-05-10 14:24:36	announced
⏵ 2	2023-11-14 08:47:37	announced	2023-11-14: Updated project metadata.

Levy R, Alter Regev T, Paes W, Gumpert N, Cohen Shvefel S, Bartok O, Dayan-Rubinov M, Alon M, Shmueli MD, Levin Y, Merbl Y, Ternette N, Samuels Y, Large-Scale Immunopeptidome Analysis Reveals Recurrent Posttranslational Splicing of Cancer- and Immune-Associated Genes. Mol Cell Proteomics, 22(4):100519(2023) [pubmed]

submitter keyword: Human, LC-MSMS, Melanoma

Yardena Samuels
contact affiliation	Department of Molecular Cell Biology The Weizmann Institute of Science Rehovot, Israel
contact email	Yardena.Samuels@weizmann.ac.il
lab head
Ronen Levy
contact affiliation	Weizmann institue
contact email	ronen.levy@weizmann.ac.il
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/2023/05/PXD034788

PRIDE project URI

• PRIDE
  1. PXD034788
     1. Label: PRIDE project
     2. Name: Large-Scale Immuno-Peptidome Analysis Reveals Recurrent Post-Translational Splicing of Cancer and Immune-Associated Genes