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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.

ABSTRACT: 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.

INSTRUMENT(S):

ORGANISM(S): Varicellovirus Human Alphaherpesvirus 1

TISSUE(S): Epithelial Cell, Cell Culture

SUBMITTER: Christoph Stingl

LAB HEAD: Theo M. Luider

PROVIDER: PXD059217 | Pride | 2025-05-28

REPOSITORIES: Pride

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Source:

			Action	DRS
	140407O2c1_LZ-0573-WO-exp--1-HSV-00_006.mgf	Mgf
	140407O2c1_LZ-0573-WO-exp--1-HSV-00_006.mzxml	Mzxml
	140407O2c1_LZ-0573-WO-exp--1-HSV-00_006.raw	Raw
	140407O2c1_LZ-0573-WO-exp--1-HSV-00_006peptides.pep.xml	Pepxml
	140407O2c1_LZ-0573-WO-exp--1-HSV-00_006peptides_1_1_0.mzid.gz	Mzid

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Project description:The overall goal of the study was to use in vivo data combined with functional genomics to define gene expression signatures representative of a spectrum of HSV CNS infections. Innate immune deficiencies result in a spectrum of severe clinical outcomes following infection. In particular, there is a strong association between loss of the signal transducer and activator of transcription (Stat) pathway, breach of the blood-brain barrier (BBB), and virus-induced neuropathology. The gene signatures that characterize resistance, disease, and mortality in the virus-infected nervous system have not been defined. Herpes simplex virus type 1 (HSV-1) is commonly associated with encephalitis in humans, and humans and mice lacking Stat1 display increased susceptibility to HSV central nervous system (CNS) infections. In this study, two HSV-1 strains were used, KOS (wild type [WT]), and Δvhs, an avirulent recombinant lacking the virion host shutoff (vhs) function. In addition, two mouse strains were used: strain 129 (control) and a Stat1-deficient (Stat1(-/-)) strain. Using combinations of these virus and mouse strains, we established a model of infection resulting in three different outcomes: viral clearance without neurological disease (Δvhs infection of control mice), neurological disease followed by viral clearance (Δvhs infection of Stat1(-/-) mice and WT infection of control mice), or neurological disease followed by death (WT infection of Stat1(-/-) mice). Through the use of functional genomics on the infected brain stem and liver, we determined gene signatures that were representative of the three infection outcomes. Gender matched, 6- to 8- week old immunocompetent, control 129S6 and 129S6 Stat1 knockout mice were infected corneally with 2x10^6 PFU of either wild type HSV-1, a vhs-null HSV virus, or mock-infected. Brain stems and liver of individual mice were isolated at days 1, 3, 5 and 7 post-inoculation for microarray analysis. For microarray analysis, samples were collected from n=2 animals (1 male, 1 female) per mouse strain and virus strain for each time point. Equal masses of tissue were pooled from two mock-infected mice per time point and run on microarray.

Dataset Information

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.

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