PXD050454-1
PXD050454 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules |
| Description | The protein corona, a dynamic biomolecular layer that forms on nanoparticle (NP) surfaces upon exposure to biological fluids is emerging as a valuable diagnostic tool for improving plasma proteome coverage analyzed by liquid chromatography-mass spectrometry (LC-MS/MS). Here, we show that spiking small molecules, including metabolites, lipids, vitamins, and nutrients, into plasma can induce diverse protein corona patterns on otherwise identical NPs, significantly enhancing the depth of plasma proteome profiling. The protein coronas on polystyrene NPs when exposed to plasma treated with an array of small molecules (n=10) allowed for detection of 1793 proteins marking an 8.25-fold increase in the number of quantified proteins compared to plasma alone (218 proteins) and a 2.63- fold increase relative to the untreated protein corona (681 proteins). Furthermore, we discovered that adding 1000 ug/ml phosphatidylcholine could singularly increase the number of unique proteins within the protein corona (897 proteins). This specific concentration of phosphatidylcholine selectively depleted the four most abundant plasma proteins, including albumin, thus reducing concentration dynamic range of plasma proteome and boosting LC-MS/MS sensitivity for detection of proteins with lower abundance. By employing an optimized data-independent acquisition (DIA) approach, the inclusion of phosphatidylcholine led to the detection of 1436 proteins in plasma. This significant achievement is made utilizing only a single NP type and one small molecule to analyze a single plasma sample, setting a new standard in proteomic depth of the plasma sample. Given the critical role of plasma proteomics in biomarker discovery and disease monitoring, we anticipate widespread adoption of this methodology for identification and clinical translation of proteomic biomarkers into FDA approved diagnostics. |
| HostingRepository | MassIVE |
| AnnounceDate | 2024-11-07 |
| AnnouncementXML | Submission_2024-11-07_09:34:53.707.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Amirata Saei |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | Orbitrap Fusion Lumos; Orbitrap Exploris 480 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-03-07 09:54:34 | ID requested | |
| ⏵ 1 | 2024-11-07 09:34:54 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Phosphatidylcholine, Nanoparticle Protein Corona, Albumin depletion |
Contact List
| Amir Ata Saei | |
|---|---|
| contact affiliation | Biozentrum, University of Basel |
| contact email | amir.saei@unibas.ch |
| lab head | |
| Amirata Saei | |
| contact affiliation | Karolinska Institutet |
| contact email | amirata.saei.dibavar@ki.se |
| 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.ucsd.edu/v07/MSV000094257/ |
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