PXD062667

PXD062667 is an original dataset announced via ProteomeXchange.

Title	Identification of Small Open Reading Frame-encoded Peptides by an Optimized Proteomics Strategy
Description	Small open reading frame-encoded peptides (SEPs) are translated from genome sequences previously unannotated, and they are now recognized as key participants in many physiological and pathological processes. Although ribosome profiling and bioinformatics analysis could predict a large number of SEPs, mass spectrometry (MS) is the only method for their direct identification. However, MS-based SEP discovery is challenged by the short length and relatively low abundance of SEPs. Thus, there is a critical need to enhance MS approaches for SEP investigations. In this study, we successfully developed an effective ammonium formate-mediated C8 solid-phase enrichment (AmF-C8-SPE). Compared to the traditional enrichment approach of Classic-C8, AmF-C8-SPE identified much more SEPs with a higher ratio of unique peptides and a boosted sequence coverage. Utilizing AmF-C8-SPE for 18 pairs of glioma tumors and adjacent normal tissues, we discovered 549 novel SEPs, and 113 of them exhibited differential expression. Importantly, randomly selected SEPs were validated by MS spectral comparison with synthetic peptides and by confirming fusion protein expression in the cells. Furthermore, Mfuzz clustering and ROC curve analyses revealed the SEPs associated with glioma progression. Finally, DeepLoc analyses predicted subcellular locations of these 549 SEPs, two of which were experimentally confirmed in the nucleus by confocal microscopy. Therefore, this study presents an effective SEP identification approach and profiles SEPs in glioma for the first time, offering valuable resources to discover glioma biomarkers/therapeutic targets.
HostingRepository	iProX
AnnounceDate	2025-04-06
AnnouncementXML	Submission_2025-04-07_00:24:52.494.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tingting Zhang
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-07 00:24:28	ID requested
⏵ 1	2025-04-07 00:24:52	announced

Dataset with its publication pending

submitter keyword: Small open reading frame-encoded peptides (SEPs), SEP enrichment, Glioma, Mass spectrometry

Yong Peng
contact affiliation	Center for Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University
contact email	yongpeng@scu.edu.cn
lab head
Tingting Zhang
contact affiliation	State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University
contact email	ttcpu2012@126.com
dataset submitter

iProX dataset URI