Dataset Information

VPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics

ABSTRACT: 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.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Joerg Doellinger

LAB HEAD: Peter Lasch

PROVIDER: PXD055135 | Pride | 2025-08-04

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 99

Publications

vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics.

Grossegesse Marica M Horn Fabian F Kurth Andreas A Lasch Peter P Nitsche Andreas A Doellinger Joerg J

Nature communications 20250731 1

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 ...[more]

PMID: 40744923

Similar Datasets

Project description:Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n= 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods. The SMAvirusChip v2 microarray includes more than 15,000 oligonucleotide probes (60-mers long) for the detection of viruses transmitted by small mammals and arthropods. The sequences of 4943 viral probes for the detection of 416 viruses (112 viruses transmitted by small mammals and 304 arboviruses) were included in this platform. Positive and negative control oligonucleotide probes were also included in the design.

Project description:Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n= 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods. The SMAvirusChip v1 microarray includes more than 15,000 oligonucleotide probes (60-mers long) for the detection of viruses transmitted by small mammals and arthropods. The sequences of 4209 viral probes for the detection of 409 viruses (109 viruses transmitted by small mammals and 300 arboviruses) were included in this platform. Positive and negative control oligonucleotide probes were also included in the design.

			Action	DRS
	Carry-over_Test.zip	Other
	PRIDE_Ebola_Plasma.zip	Other
	PRIDE_SARS-CoV-2_Swab.zip	Other
	Sensitivity_Panel.zip	Other
	Specificity_Panel.zip	Other