PXD059217

PXD059217 is an original dataset announced via ProteomeXchange.

Title	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.
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.
HostingRepository	PRIDE
AnnounceDate	2025-05-28
AnnouncementXML	Submission_2025-05-28_00:32:27.693.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD059217
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Christoph Stingl
SpeciesList	scientific name: Varicellovirus; NCBI TaxID: 10319; scientific name: Human alphaherpesvirus 1; NCBI TaxID: 10298;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap XL; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-24 06:55:25	ID requested
⏵ 1	2025-05-28 00:32:28	announced

10.6019/PXD059217;

submitter keyword: retinal pigment epithelial cells,varicella-zoster virus, mass-spectrometry, software, herpes simplex virus 1, epidermal growth factor

Theo M. Luider
contact affiliation	Head of Laboratory of Neuro-Oncology, Neurology, Clinical & Cancer Proteomics
contact email	t.luider@erasmusmc.nl
lab head
Christoph Stingl
contact affiliation	Erasmus MC Rotterdam Department of Neurology
contact email	c.stingl@erasmusmc.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD059217
     1. Label: PRIDE project
     2. Name: 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.