PXD016981

PXD016981 is an original dataset announced via ProteomeXchange.

Title	Deeply mining a universe of peptides Encoded by Long Noncoding RNAs
Description	Long non-coding RNAs (lncRNAs) are generally defined as RNA transcripts longer than 200 nucleotides that are not translated into proteins. Recently, many small open reading frames (smORFs) embedded in lncRNA scripts have been verified to be able to encode functional polypeptides (namely lncRNA-SEPs here). Although collaborative analysis by advanced genomics, bioinformatics and proteomics largely drives SEPs discovery, the poor predictability, diminutive size and low abundance still challenge systematic identification of SEPs from different biological samples. Here, we took advantage of the NONCODE database that deposited with the most complete collection and annotation of lncRNA transcripts from different species to build a database that to maximally collect all putative small ORFs from human and mouse lncRNA transcripts. Two effective and complementary polypeptides enrichment strategies (30 kDa MWCO filter and C8 SPE column) were also integrated to further improve the discovery of novel lncRNA-SEPs. These efforts led to the discovery of 362 lncRNA-SEPs from 8 human cell lines and 238 lncRNA-SEPs from 3 mouse cell lines and 8 mouse tissues. 18 out of these lncRNA-SEPs were verified experimentally by multiple technologies including in vitro expression, immunoblotting and parallel reaction monitoring-based mass spectrometry (PRM-MS) in 293T cells. Further bioinformatic analysis reveals that the physical and chemical properties of these novel lncRNA-SEPs, such as amino acid composition and codon usage, are varied from canonical proteins. Intriguingly, nearly 70% of the identified lncRNA-SEPs were found to be initiated with non-AUG start codons. Collectively, the efficient workflows presented in this study enables us identify 600 novel lncRNA-SPEs from multiple cell lines and tissues, which should represent the largest number of MS-detected lncRNA-encoding SEPs ever reported to date. These novel lncRNA-SEPs not only could provide new clues for the annotation of the noncoding elements in the genome, but also could serve as a valuable resource for the functional characterization of individual lncRNA-SEPs.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:45:26.688.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Qing Zhang
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; 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	2020-01-07 03:59:21	ID requested
1	2023-05-06 03:27:46	announced
⏵ 2	2023-11-14 08:45:35	announced	2023-11-14: Updated project metadata.

Cai T, Zhang Q, Wu B, Wang J, Li N, Zhang T, Wang Z, Luo J, Guo X, Ding X, Xie Z, Niu L, Ning W, Fan Z, Chen X, Guo X, Chen R, Zhang H, Yang F, LncRNA-encoded microproteins: A new form of cargo in cell culture-derived and circulating extracellular vesicles. J Extracell Vesicles, 10(9):e12123(2021) [pubmed]

submitter keyword: lncRNA, mass spectrometry, smORF, enrichment, SEPs

Fuquan Yang
contact affiliation	Institute of Biophysics, Chinese Academy of Sciences
contact email	fqyang@ibp.ac.cn
lab head
Qing Zhang
contact affiliation	Institute of Biophysics, Chinese Academy of Sciences
contact email	zhangqing14@mails.ucas.ac.cn
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/PXD016981

PRIDE project URI

• PRIDE
  1. PXD016981
     1. Label: PRIDE project
     2. Name: Deeply mining a universe of peptides Encoded by Long Noncoding RNAs