PXD044809 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
Publication List
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] |
Keyword List
submitter keyword: protein isoform,Shotgun proteomics, quantification |
Contact List
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 | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD044809
- Label: PRIDE project
- Name: SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics