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PXD044809

PXD044809 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics
DescriptionShotgun 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_06:09:09.795.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterYongchao Dou
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-08-23 12:23:16ID requested
12023-10-24 11:33:26announced
22023-11-14 09:07:48announced2023-11-14: Updated project metadata.
32024-10-22 06:09:13announced2024-10-22: 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 affiliationBaylor College of Medicine
contact emailbing.zhang@bcm.edu
lab head
Yongchao Dou
contact affiliationBaylor college of medicine
contact emailyongchao.dou@bcm.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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