PXD057159-1

PXD057159 is an original dataset announced via ProteomeXchange.

Title	P4PP: an universal shotgun proteomics data analysis pipeline for virus identification
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.
HostingRepository	PRIDE
AnnounceDate	2025-05-28
AnnouncementXML	Submission_2025-05-28_08:26:45.055.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jiri DRESLER
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Chlorocebus sabaeus; NCBI TaxID: 60711; scientific name: Orthopoxvirus; NCBI TaxID: 10242;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-24 11:10:02	ID requested
⏵ 1	2025-05-28 08:26:45	announced

Dataset with its publication pending

submitter keyword: Orthopoxviruses, LC-MS/MS

Jiri Dresler
contact affiliation	Military Health Institute, Military Medical Agency, 16200 Prague, Czech Republic
contact email	jiri.dresler@gmail.com
lab head
Jiri DRESLER
contact affiliation	Military Health Institute, Prague/Czech Republic
contact email	jiri.dresler@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD057159
     1. Label: PRIDE project
     2. Name: P4PP: an universal shotgun proteomics data analysis pipeline for virus identification