PXD060784-1

PXD060784 is an original dataset announced via ProteomeXchange.

Title	Mass Spectrometry-Based Top-Down Proteomics for Proteoform Profiling of Protein Corona
Description	The protein corona, a layer of biomolecules—primarily proteins—that adsorb to nanoparticle (NP) surfaces in biological fluids, critically affects NP safety and their therapeutic and diagnostic functions. Additionally, the protein corona effectively reduces proteome complexity and the dynamic range of protein concentrations in blood plasma and other complex fluids. By suppressing highly abundant proteins, the protein corona enhances the potential for biomarker discovery across diverse health conditions, thereby advancing diagnostic and therapeutic applications. Traditionally, protein corona studies have relied on mass spectrometry (MS)-based bottom-up proteomics (BUP) to analyze corona composition. However, BUP approaches do not accurately identify specific proteoforms—distinct molecular variants of proteins—within the corona. This limitation impedes the nanomedicine field’s ability to precisely predict the biological fate and pharmacokinetics of nanomedicines, as well as their effectiveness in early-stage biomarker discovery and disease detection. Here, we present protocols utilizing capillary zone electrophoresis (CZE)-MS-based top-down proteomics (TDP) to characterize the proteoform landscape of the protein corona. Our procedures detail the recovery of intact proteoforms from NP surfaces and the measurement of these proteoforms using CZE-MS/MS and CZE-high-field asymmetric waveform ion mobility spectrometry (FAIMS)-MS/MS. The entire workflow is completed within three to four days. Implementing this protocol offers mechanistic insights into how proteoforms modulate NP–bio interactions, enabling the nanomedicine community to acquire more comprehensive protein corona profiles. This advancement has the potential to significantly enhance the diagnostic and therapeutic efficacy of nanomedicine technologies.
HostingRepository	PRIDE
AnnounceDate	2025-09-08
AnnouncementXML	Submission_2025-09-07_16:36:54.352.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Liangliang Sun
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-13 12:13:57	ID requested
⏵ 1	2025-09-07 16:36:55	announced

Sadeghi SA, Fang F, Tabatabaeian Nimavard R, Wang Q, Zhu G, Saei AA, Sun L, Mahmoudi M, Mass spectrometry-based top-down proteomics for proteoform profiling of protein coronas. Nat Protoc, ():(2025) [pubmed]

10.1038/s41596-025-01229-6;

submitter keyword: top-down proteomics, mass spectrometry, nanomedicine,protein corona

Liangliang Sun
contact affiliation	Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
contact email	lsun@chemistry.msu.edu
lab head
Liangliang Sun
contact affiliation	Michigan State University
contact email	lsun@chemistry.msu.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD060784
     1. Label: PRIDE project
     2. Name: Mass Spectrometry-Based Top-Down Proteomics for Proteoform Profiling of Protein Corona