PXD036663

PXD036663 is an original dataset announced via ProteomeXchange.

Title	Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification
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.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_06:42:26.581.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD036663
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Armand Paauw
SpeciesList	scientific name: Macaca mulatta (Rhesus macaque); NCBI TaxID: 9544; scientific name: Cercopithecus aethiops (Green monkey) (Grivet); NCBI TaxID: 9534; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-12 06:32:52	ID requested
1	2023-06-16 06:41:54	announced
⏵ 2	2023-11-14 06:42:27	announced	2023-11-14: Updated project metadata.

10.6019/PXD036663;

submitter keyword: diagnsoe, proteomics, identification, virus, proteome2virus,mass spectrometry

Dr. ir. A.M.J. (Annette) Kliphuis
contact affiliation	Research Manager, TNO, Department CBRN protection, The Netherlands (lab head) (lab head)
contact email	annette.kliphuis@tno.nl
lab head
Armand Paauw
contact affiliation	TNO
contact email	armand.paauw@tno.nl
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/2023/06/PXD036663

PRIDE project URI

• PRIDE
  1. PXD036663
     1. Label: PRIDE project
     2. Name: Proteome2virus: Shotgun mass spectrometry data analysis pipeline for virus identification