PXD044809

PXD044809 is an original dataset announced via ProteomeXchange.

Title	SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics
Description	Shotgun proteomics is essential for protein identification and quantification in biomedical research, but protein isoform characterization is challenging due to the extensive number of peptides shared across proteins, hindering our understanding of protein isoform regulation and their roles in normal and disease biology. We systematically assess the challenge and opportunities of shotgun proteomics-based protein isoform characterization using in silico and experimental data, and then present SEPepQuant, a graph theory-based approach to maximize isoform characterization. Using published data from one induced pluripotent stem cell study and two human hepatocellular carcinoma studies, we demonstrate the ability of SEPepQuant in addressing the key limitations of existing methods, providing more comprehensive isoform-level characterization, identifying hundreds of isoform-level regulation events, and facilitating streamlined cross-study comparisons. Our analysis provides solid evidence to support a widespread role of protein isoform regulation in normal and disease processes, and SEPepQuant has broad applications to biological and translational research.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:09:09.795.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yongchao Dou
SpeciesList	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	2023-08-23 12:23:16	ID requested
1	2023-10-24 11:33:26	announced
2	2023-11-14 09:07:48	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 06:09:13	announced	2024-10-22: Updated project metadata.

10.1038/s41467-023-41558-2;

Dou Y, Liu Y, Yi X, Olsen LK, Zhu H, Gao Q, Zhou H, Zhang B, SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics. Nat Commun, 14(1):5809(2023) [pubmed]

submitter keyword: protein isoform,Shotgun proteomics, quantification

Bing Zhang
contact affiliation	Baylor College of Medicine
contact email	bing.zhang@bcm.edu
lab head
Yongchao Dou
contact affiliation	Baylor college of medicine
contact email	yongchao.dou@bcm.edu
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/2023/10/PXD044809

PRIDE project URI

• PRIDE
  1. PXD044809
     1. Label: PRIDE project
     2. Name: SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics