Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

P4PP: an universal shotgun proteomics data analysis pipeline for virus identification, samples of DGA CBRN Defence Center

ABSTRACT: Humans can be infected by a wide variety of virus species. To detect these different viruses, a data analysis approach for shotgun proteomic data was developed. For this proteome for pandemic preparedness (P4PP) pipeline, a database (P4PPv01) and a web application (P4PP) were constructed. The P4PP pipeline enables the identification of 1896 virus species from the 32 virus families in which at least one human-infectious virus is described. To evaluate the developed analysis pipeline the supernatant of Vero Cell cultures of three Togaviridae (Rio Negro virus, Sindbis virus and Pixuna virus) and a negative sample were analyzed.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Cercopithecus Aethiops (green Monkey) (grivet) Sindbis Virus Rio Negro Virus Pixuna Virus

TISSUE(S): Kidney Epithelial Cell, Cell Culture

SUBMITTER: Marine Eschlimann

LAB HEAD: Vincent Ramisse

PROVIDER: PXD057670 | Pride | 2025-06-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	VERO-E6-140922_01.mgf	Mgf
	VERO-E6-140922_01.mzxml	Mzxml
	VERO-E6-140922_01.raw	Raw
	VERO-E6-140922_01peptides.pep.xml	Pepxml
	VERO-E6-140922_01peptides_1_1_0.mzid.gz	Mzid

Items per page:

1 - 5 of 21

Similar Datasets

Proteome4Pandemic Preparedness: Proteomics, an agnostic approach to identify virusesProteome4Pandemic Preparedness: Proteomics, an agnostic approach to identify viruses

2025-05-27 | PXD054958 | Pride

Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification

Project description:To increase the number of virus species that can be detected we developed a shotgun proteomics based approach, which was applied to viral samples, after which the identified peptides were searched for in a database equipped with proteomic data of 46 viruses, known to be infectious to humans, using a web application (‘proteome2virus.com’). To validate proteome2virus application (proteome2virus.com) data of cultured and clinical samples was generated. The method has been successfully tested against cultured viruses and 8 clinical fecales samples of 10 different viral species from 7 different virus families, including SARS-CoV-2, Betacoronavirus OC43, human coronavirus 229E, human orthopneumovirus (RSV A and RSV B), human metapneumovirus, Influenza A (H1N1 and H3N2), mamastrovirus 1, Norwalk virus, Rotavirus A and human mastadenovirus F, representing 7 different virus families. The samples were prepared with two different sample preparation methods and were measured on two different mass spectrometers. Results demonstrated that the developed data analysis pipeline is applicable to different MS data sets generated on 2 different instruments and that it this approach identifies a high variety of clinically relevant viral species. This emphasizes the potential and feasibility for the diagnosis of a wide range of viruses in clinical samples with a single shotgun proteomics analysis.

2023-06-16 | PXD036663 | Pride

Sindbis survivors

Project description:Microarray analysis comparing cells that are resistant to Sindbis virus-induced cell death (clones 9, 43) versus cells that are sensitive to Sindbis virus-induced cell death (WT293) Keywords = Sindbis alphavirus functinal phenotype Keywords: repeat sample

2004-05-01 | GSE1264 | GEO

Transcription profiling of resistant and sensitive human cell lines infected with Sindbis virus

2007-08-03 | E-GEOD-1264 | biostudies-arrayexpress

Transcriptome analysis of tumors isolated from ovarian cancer tumor bearing mice treated with Sindbis Virus vectors and untreated controls

Project description:Gene expression analysis of tumors isolated from mice after they received treatments with Sindbis Virus vectors for 1 week. The hypothesis tested changes in the transcriptome profiles of tumors isolated from Sindbis virus vectors treated and untreated mice. Expression profiling by high throughput sequencing of MOSEC.Fluc.p11 tumors

2022-12-20 | GSE216750 | GEO

Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification in data subset of Ouwendijk et al. 2020, Analysis of Virus and Host Proteomes During Productive HSV-1 and VZV Infection in Human Epithelial Cells.

Project description:The initial project of the data of origin is described in Ouwendijk, et al. (2020). Analysis of Virus and Host Proteomes During Productive HSV-1 and VZV Infection in Human Epithelial Cells. Frontiers in Microbiology, 11, 1179. https://doi.org/10.3389/fmicb.2020.01179. To increase the number of virus species that can be detected we developed a shotgun proteomics based approach, which was applied to viral samples, after which the identified peptides were searched for in a database equipped with proteomic data of 46 viruses, known to be infectious to humans, using a web application (‘proteome2virus.com’). To validate proteome2virus application (proteome2virus.com) data of cultured and clinical samples was generated. The method has been successfully tested against cultured viruses and 8 clinical fecales samples of 10 different viral species from 7 different virus families, including SARS-CoV-2, Betacoronavirus OC43, human coronavirus 229E, human orthopneumovirus (RSV A and RSV B), human metapneumovirus, Influenza A (H1N1 and H3N2), mamastrovirus 1, Norwalk virus, Rotavirus A and human mastadenovirus F, representing 7 different virus families. The samples were prepared with two different sample preparation methods and were measured on two different mass spectrometers. Results demonstrated that the developed data analysis pipeline is applicable to different MS data sets generated on 2 different instruments and that it this approach identifies a high variety of clinically relevant viral species. This emphasizes the potential and feasibility for the diagnosis of a wide range of viruses in clinical samples with a single shotgun proteomics analysis.

2025-05-28 | PXD059217 | Pride

Project description:Sindbis virus amplicon sequencing

| PRJNA875102 | ENA

Sindbis virus

Project description:Sindbis virus Raw sequence reads

| PRJNA361123 | ENA

The mitochondrial protease OMA1 acts as a metabolic safeguard upon nuclear DNA damage

Project description:The metabolic plasticity of mitochondria supports cell development and differentiation and ensures cell survival under stress. The peptidase OMA1 regulates mitochondrial morphology and stress signaling and orchestrates tumorigenesis and cell fate decisions in a cell and tissue-specific manner. Here, we have used unbiased systemic approaches to demonstrate that OMA1-dependent cell fate decisions are under metabolic control. A metabolism-focus CRISPR screen combined with an integrated analysis of human expression data unraveled a protective role of OMA1 against DNA damage. Nucleotide deficiencies induced by chemotherapeutic agents promote the selective, p53-dependent apoptosis of cells lacking OMA1. The protective effect of OMA1 does not depend on OMA1 activation nor on OMA1-mediated OPA1 and DELE1 processing. OMA1-deficient cells have reduced glycolytic capacity and accumulate OXPHOS proteins upon DNA damage. OXPHOS inhibition restores glycolysis and confers resistance against DNA damage. Thus, metabolic cues determine cell fate decisions by OMA1, which sheds new light on the role of OMA1 in cancerogenesis.

2023-04-04 | PXD036595 | Pride

P4PP: an universal shotgun proteomics data analysis pipeline for virus identification  

Project description:Humans can be infected by a wide variety of virus species. To detect these different viruses, a data analysis approach for shotgun proteomic data was developed. For this proteome for pandemic preparedness (P4PP) pipeline, a database (P4PPv01) and a web application (P4PP) were constructed. The P4PP pipeline enables the identification of 1896 virus species from the 32 virus families in which at least one human-infectious virus is described. P4PP was evaluated using different datasets of cell-cultivated viruses, generated at different institutes, measured with different instruments and prepared with different sample preparations methods. In total, 174 MS datasets of 160 and 14 protein trypsin digests of virus-infected and non-infected cell lines were analyzed, respectively. Of the 160 samples, 146 were correctly identified at the species level, and an additional 4 samples were identified to the family level. In the remaining 10 samples, no virus was detected. However, all these 10 samples tested positive in follow-up samples measured in that time series, indicating that the number of peptides derived from the virus was initially too low in the samples obtained at the start of the experiment. Furthermore, results show that Influenza A or SARS-CoV-2 can be subtyped if enough peptides of the virus are identified. Shotgun proteomics, in combination with the developed data analysis approach, can identify all types of virus species after cultivation in a cell line. Implementing this virus proteome analysis capability in viral diagnostic laboratories will likely improve their capabilities to cope with unexpected, mutated or re-emerging viruses.

2025-05-28 | PXD057159 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data