PXD055135-1

PXD055135 is an original dataset announced via ProteomeXchange.

Title	vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics
Description	Viral infections are commonly diagnosed by the detection of viral genome fragments or proteins using targeted methods such as PCR and immunoassays. In contrast, metagenomics enables the untargeted identification of viral genomes, expanding its applicability across a broader spectrum. In this study, we introduce proteomics as a complementary approach for the untargeted identification of human-pathogenic viruses from patient samples. The viral proteomics workflow (vPro-MS) is based on an in-silico derived peptide library covering the human virome in UniProtKB (331 viruses, 20,386 genomes, 121,977 peptides), which was especially designed for diagnostic purposes. A scoring algorithm (vProID score) was developed to assess the confidence of virus identification from proteomics data. In combination with high-throughput diaPASEF-based data acquisition, this workflow enables the analysis of up to 60 samples per day. The specificity was determined to be > 99,9 % in an analysis of 221 plasma, swab and cell culture samples covering 18 different viruses (e.g. SARS, MERS, EBOV, MPXV). The sensitivity of this approach for the detection of SARS-CoV-2 in nasopharyngeal swabs corresponds to a PCR cycle threshold of 27 with comparable quantitative accuracy to metagenomics. vPro-MS enables the integration of untargeted virus identification in large-scale proteomic studies of biofluids such as human plasma to detect previously undiscovered virus infections in patient specimens.
HostingRepository	PRIDE
AnnounceDate	2025-08-04
AnnouncementXML	Submission_2025-08-04_14:22:56.661.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joerg Doellinger
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-23 08:07:24	ID requested
⏵ 1	2025-08-04 14:22:57	announced

Grossegesse M, Horn F, Kurth A, Lasch P, Nitsche A, Doellinger J, vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics. Nat Commun, 16(1):7041(2025) [pubmed]

10.1038/s41467-025-62469-4;

submitter keyword: pathogen detection, virus identification, virome,virus

Peter Lasch
contact affiliation	Proteomics and Spectroscopy, ZBS6, Robert Koch Institute, Germany
contact email	LaschP@rki.de
lab head
Joerg Doellinger
contact affiliation	Proteomics and Spectroscopy (ZBS6), Robert Koch-Institute
contact email	Doellingerj@rki.de
dataset submitter

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://ftp.pride.ebi.ac.uk/pride/data/archive/2025/08/PXD055135

PRIDE project URI

• PRIDE
  1. PXD055135
     1. Label: PRIDE project
     2. Name: vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics