PXD010793-1

PXD010793 is an original dataset announced via ProteomeXchange.

Title	Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome
Description	Spliced peptides are short protein fragments spliced together in the proteasome by peptide bond formation. True estimation of the contribution of proteasome-spliced peptides (PSPs) to the global Human Leukocyte Antigen (HLA) ligandome is critical. A recent study suggested that PSPs contribute up to 30% of the HLA ligandome. We performed a thorough reanalysis of the reported results using multiple computational tools and various validation steps and concluded that only a fraction of the proposed PSPs passes the quality filters. To better estimate the actual number of PSPs, we present an alternative workflow. We performed de-novo sequencing of the HLA-peptide spectra and discarded all de-novo sequences found in the UniProt database. We checked whether the remaining de-novo sequences could match spliced peptides from human proteins. The spliced sequences were appended to the UniProt fasta file, which was searched by two search tools at a FDR of 1%. We find that 2-6% of the HLA ligandome could be explained as spliced protein fragments. The majority of these potential PSPs have good peptide-spectrum match properties and are predicted to bind the respective HLA molecules. However, it remains to be shown how many of these potential PSPs actually originate from proteasomal splicing events.
HostingRepository	PRIDE
AnnounceDate	2018-09-03
AnnouncementXML	Submission_2018-09-03_04:10:58.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michal Bassani-Sternberg
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-08-16 02:06:41	ID requested
⏵ 1	2018-09-03 04:10:59	announced
2	2018-12-04 04:07:24	announced	Updated project metadata.
3	2024-10-22 04:48:12	announced	2024-10-22: Updated project metadata.

Mylonas R, Beer I, Iseli C, Chong C, Pak HS, Gfeller D, Coukos G, Xenarios I, M, ü, ller M, Bassani-Sternberg M, Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome. Mol Cell Proteomics, 17(12):2347-2357(2018) [pubmed]

submitter keyword: Immunopeptidomics, HLA-I peptides, LC-MSMS, Proteasomal splicing

Michal Bassani-Sternberg
contact affiliation	Center of experimental therapeutics Department of oncology UNIL CHUV Ludwig Institute for Cancer Research Lausanne Biopôle 3 Chemin des Boveresses 155, CH-1066 Lausanne
contact email	michal.bassani@chuv.ch
lab head
Michal Bassani-Sternberg
contact affiliation	UNIL/CHUV
contact email	michal.bassani@chuv.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/2018/09/PXD010793

PRIDE project URI

• PRIDE
  1. PXD010793
     1. Label: PRIDE project
     2. Name: Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome