PXD050454

PXD050454 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-07 09:54:34	ID requested
⏵ 1	2024-11-07 09:34:54	announced

no publication

submitter keyword: Phosphatidylcholine, Nanoparticle Protein Corona, Albumin depletion

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

MassIVE dataset URI

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