PXD058001-1
PXD058001 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Depletion of Abundant Plasma Proteins in Human Serum via in situ Protein@ZIF-8 Synthesis for Integrated Proteomics |
| Description | Protein biomarkers in human serum provide critical insights into various physiological conditions and diseases, enabling early diagnosis, prognosis, and personalized treatment. However, detecting low-abundance protein biomarkers is challenging due to the presence of highly abundant proteins that make up ~99% of the plasma proteome. Here, we report for the first time the use of in situ metal-organic-framework (MOF) growth in serum to effectively deplete highly abundant serum proteins for integrated proteomic analysis. Through biomolecule-mediated nucleation of a zeolitic imidazolate framework (ZIF-8), abundant plasma proteins are selectively encapsulated within ZIF-8 and removed from serum via centrifugation, leaving a depleted protein fraction in the supernatant. Bottom-up proteomics analysis confirmed significant depletion of the topmost abundant proteins, many at depletion levels exceeding 95%. Such depletion enabled the identification of 277 total proteins in the supernatant (uncaptured) fraction in a single-shot analysis, including 54 uniquely identified proteins, 12 drug targets, and many potential disease biomarkers. Top-down proteomics characterization of the captured and uncaptured protein fractions at the proteoform-level confirmed this method is not biased toward any specific proteoform of individual proteins. These results demonstrate that in situ MOF growth can selectively and effectively deplete high-abundance proteins from serum in a simple, low-cost, one-pot synthesis to enable integrated top-down and bottom-up proteomic analysis of serum protein biomarkers. |
| HostingRepository | MassIVE |
| AnnounceDate | 2025-05-22 |
| AnnouncementXML | Submission_2025-05-22_10:49:16.677.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Hsin-Ju Chan |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Oxidation; cysteinylation (disulfide with free L-cysteine); Acetyl; hexose glycated L-lysine |
| Instrument | timsTOF Pro; impact II |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-11-18 10:40:03 | ID requested | |
| ⏵ 1 | 2025-05-22 10:49:17 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: metal-organic framework, human serum proteomics, protein separation, bottom-up proteomics, top-down proteomics, biomarker discovery, depletion technology, DatasetType:Proteomics |
Contact List
| Ying Ge | |
|---|---|
| contact affiliation | University of Wisconsin-Madison |
| contact email | ge2@wisc.edu |
| lab head | |
| Hsin-Ju Chan | |
| contact affiliation | University of Wisconsin-Madison |
| contact email | hchan48@wisc.edu |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| 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://massive-ftp.ucsd.edu/v07/MSV000096453/ |
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