PXD020620

PXD020620 is an original dataset announced via ProteomeXchange.

Title	LC-MSMS of 3 DLBCL cell lines (class I immunopeptidome and whole proteome)
Description	Accumulating evidence indicates that alternative translation events occur in all cell types, suggesting that the proteome is more complex than previously anticipated. We elected to broaden the repertoire of human cryptic proteins by designing an approach combining ribosome profiling, which gives a precise view of truly active translation events, and mass spectrometry, which is so far the best way to screen with confidence the cellular proteome. This allowed building complete but noiseless customized protein databases suitable for MS-based protein identification. The analysis of the immunopeptidome and whole proteome of DLBCL cell lines led to the identification of 710 novel protein isoforms along with 1856 new cryptic proteins, from which 72% derived from allegedly non-coding regions of the genome. Globally, cryptic proteins were very distinct from canonical proteins, as they were shorter, less stable, initiated at a diversified set of start codons and were at least 5-fold more efficient for MHC-I peptide generation. The translation efficiency of novel isoforms and cryptic proteins was at least as good as for canonical proteins and we propose that some of them could regulate the translation of canonical proteins involved in cellular stress and cancer cell growth.
HostingRepository	PRIDE
AnnounceDate	2020-11-16
AnnouncementXML	Submission_2020-11-16_14:41:58.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD020620
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Eric Bonneil
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; deamidated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-28 17:51:19	ID requested
⏵ 1	2020-11-16 14:41:58	announced

Dataset with its publication pending

submitter keyword: DLBCL, LC-MSMS, MHC class I, immunopeptidome, proteome, HBL-1, DoHH2, and SU-DHL-4

Claude Perreault
contact affiliation	IRIC-Université de Montréal
contact email	claude.perreault@umontreal.ca
lab head
Eric Bonneil
contact affiliation	Proteomic Platform
contact email	eric.bonneil@umontreal.ca
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/2020/11/PXD020620

PRIDE project URI

• PRIDE
  1. PXD020620
     1. Label: PRIDE project
     2. Name: LC-MSMS of 3 DLBCL cell lines (class I immunopeptidome and whole proteome)