PXD038602 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Glycosylation Profiling of Neoplastic Biomarker Alpha Fetoprotein Through Intact Mass Protein Analysis |
Description | Glycosylation is an important post-translational modification (PTM) mechanism of proteins, that modulates protein function. Measurement of clinically adopted cancer protein biomarkers is commonly performed using affinity-based techniques, which often suffer from poor specificity and inability to distinguish between closely related proteoforms. Alpha fetoprotein (AFP) is a circulating cancer biomarker implicated in multiple neoplastic malignancies, including hepatocellular carcinoma (HCC). AFP glycoforms with core fucosylation structure (AFP-L3) are used clinically as a biomarker, to predict risk of developing HCC and to monitor its recurrence. Mature AFP has a single glycosylation site, while there is a high degree of structural variation in AFP-glycan modifications. Because AFP has single glycosylation site, masses of intact AFP proteoforms can be used to differentiate and identify PTM in their native states. We developed a method for intact AFP glycoform analysis that utilizes AFP-specific immune-enrichment, followed by LC-high resolution mass spectrometry (LC-HRMS) analysis to differentiate and quantitate the relative abundance of AFP glycoforms and evaluated the method’s performance. |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_08:25:50.982.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Mark Kushnir |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | phosphorylated residue; complex glycosylation |
Instrument | 6550 iFunnel Q-TOF LC/MS |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-12-07 03:33:40 | ID requested | |
1 | 2023-01-11 15:06:46 | announced | |
⏵ 2 | 2023-11-14 08:25:52 | announced | 2023-11-14: Updated project metadata. |
Publication List
Dunbar C, Kushnir MM, Yang YK, Glycosylation Profiling of the Neoplastic Biomarker Alpha Fetoprotein through Intact Mass Protein Analysis. J Proteome Res, 22(1):226-234(2023) [pubmed] |
Keyword List
submitter keyword: intact proteins,hepatocellular carcinoma |
Contact List
Yifei Yang |
contact affiliation | Mayo Clinic |
contact email | yang.yifei@mayo.edu |
lab head | |
Mark Kushnir |
contact affiliation | ARUP Institute for Clinical & Experimental Pathology |
contact email | kushnmm@aruplab.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD038602
- Label: PRIDE project
- Name: Glycosylation Profiling of Neoplastic Biomarker Alpha Fetoprotein Through Intact Mass Protein Analysis