PXD025813

PXD025813 is an original dataset announced via ProteomeXchange.

Title	Identification and analysis of small proteins and short open reading frame encoded peptides in Hep3B cell
Description	The small proteins and short open reading frames encoded peptides (SEPs) are of fundamental importance because of their essential roles in biological processes. However, the annotation or identification of them is challenging, in part owing to the limitation of the traditional genome annotation pipeline and their inherent characteristics of low abundance and low molecular weight. To discover and characterize SEPs in Hep3B cell line, we developed an optimized peptidomic assay by combining different peptide extraction and separation methods. The organic solvent precipitation method in peptidomic showed promotion in the enrichment of low molecular proteins or peptides, and the data clearly showed a beneficial effect from the reduction of sample complexity, resulting in high-quality MS/MS spectra. Furthermore, different strategies exhibited good complementarity in improving the total amount of small proteins and their sequence coverage. In total, 1192 proteins within less than 100 amino acids were identified, including 271 newly discovered SEPs that been annotated in the OpenProt database and 147 SEPs of them encoded from ncRNA or lincRNA. Results in this work provide robust evidence to date that the human proteome is more complicated than previously appreciated, and this will be a benefit to discoveries of proteins without function annotation. SIGNIFICANCE: In this work, methods were optimized to identify SEPs in Hep3B. The organic solvent precipitation presents promotion in enrichment of low molecular proteins or peptides, and the data clearly showed a beneficial effect from the reduction of sample complexity, resulting in high quality MS/MS spectra. Different strategies exhibited good complementarity in improving total amount of small proteins and their sequence coverage. In total, 1192 proteins within less than 100 amino acids were identified, including 271 newly discovered SEPs that been annotated in the OpenProt database and 147 SEPs of them encoded from ncRNA or lincRNA. Furthermore, 22 SEPs generated from the uORF may has potential effect in translation control, and 149 newly identified SEPs have known functional domains or cross-species conservation. Results in this work present robust evidence for the coding potential of the ignored region of human genomes and may provide additional insights into tumor biology.
HostingRepository	iProX
AnnounceDate	2021-05-05
AnnouncementXML	Submission_2021-05-05_21:06:01.943.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Bing Wang
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-05 21:04:57	ID requested
⏵ 1	2021-05-05 21:06:03	announced

Wang B, Hao J, Pan N, Wang Z, Chen Y, Wan C, Identification and analysis of small proteins and short open reading frame encoded peptides in Hep3B cell. J Proteomics, 230():103965(2021) [pubmed]

submitter keyword: Acetonitrile precipitation, Hep3B cell line, Peptidomic

SEP enrichment, Short open reading frames, sORF-encoded peptides.

Cuihong Wan
contact affiliation	Central China Normal University
contact email	ch_wan@mail.ccnu.edu.cn
lab head
Bing Wang
contact affiliation	Central China Normal University
contact email	635819601@qq.com
dataset submitter

iProX dataset URI