PXD019486

PXD019486 is an original dataset announced via ProteomeXchange.

Title	Long noncoding RNA (lncRNA), smORF encoded polypeptides (SEPs), NONCODE database, enrichment, mass spectrometry
Description	Many small open reading frames (smORFs) embedded in lncRNA transcripts have been shown to encode biologically functional polypeptides (smORFs-encoded polypeptides, SEPs) in different organisms. Despite significant advances in genomics, bioinformatics and proteomics that largely enabled the discovery of novel SEPs, their identification across different biological samples is still hampered by their poor predictability, diminutive size and low relative abundance. Here, we take advantage of NONCODE, a repository containing the most complete collection and annotation of lncRNA transcripts from different species, to build a novel database that attempts to maximize a collection of SEPs from human and mouse lncRNA transcripts. In order to further improve SEP discovery, we implemented two effective and complementary polypeptide enrichment strategies, 30 kDa MWCO filter and C8 SPE column. These combined strategies enabled us to discover 357 and 409 SEPs from, respectively, 8 human cell lines, and 3 mouse cell lines and 8 mouse tissues. Importantly, nineteen of the identified SEPs were then verified through in-vitro expression, immunoblotting, parallel reaction monitoring (PRM) and synthetic peptides. Subsequent bioinformatic analysis revealed that some of the physical and chemical properties of these novel SEPs, including amino acid composition and codon usage, are different from those commonly found in canonical proteins. Intriguingly, nearly 65% of the identified SEPs were found to be initiated with non-AUG start codons. Overall, the strategy presented in this study encompasses an efficient workflow that enabled us to identify 766 novel SEPs across multiple cell lines and tissues, which probably represents the largest number of SEPs detected by mass spectrometry reported to date. These novel SEPs might not only provide new clues for the annotation of noncoding elements in the genome but can also serve as a valuable resource for the functional characterization of individual SEPs.
HostingRepository	PRIDE
AnnounceDate	2021-06-15
AnnouncementXML	Submission_2021-06-14_18:26:11.050.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	2020-06-01 03:10:44	ID requested
⏵ 1	2021-06-14 18:26:11	announced

Dataset with its publication pending

submitter keyword: Long noncoding RNA (lncRNA), smORF encoded polypeptides (SEPs), NONCODE database, enrichment, mass spectrometry

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/2021/06/PXD019486

PRIDE project URI

• PRIDE
  1. PXD019486
     1. Label: PRIDE project
     2. Name: Long noncoding RNA (lncRNA), smORF encoded polypeptides (SEPs), NONCODE database, enrichment, mass spectrometry