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PXD019648

PXD019648 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleLC-MSMSMass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein
DescriptionDetection of viral RNA by PCR is currently the main diagnostic tool for COVID-191. The PCR-based test, however, shows limited sensitivity, especially at early and late stages of the disease development, and is relatively time consuming. Fast and reliable complementary methods for detecting the viral infection would be of help in the current pandemia conditions. Mass-spectrometry is one of such possibilities. We have developed a mass-spectrometry based method for the detection of the SARS CoV-2 virus in nasopharynx epithelial swabs, based on the detection of the viral nucleocapsid N protein. The N protein of the SARS-COV-2 virus, the most abundant protein in the virion, is the best candidate for mass-spectrometric detection of the infection, and MS-based detection of several peptides from the SARS-COoV-2 nucleoprotein has been reported earlier by the Sinz group. Our approach shows confident identification of the N protein in patient samples even with the lowest viral loads and a much simpler preparation procedure. Our main protocol consists of virus inactivation by heating and adding of isopropanol, and tryptic digestion of the proteins sedimented from the swabs followed by MS analysis. A set of unique peptides, produced as a result of proteolysis of the nucleocapsid phosphoprotein of SARS-CoV-2, is detected. The obtained results can further be used to create fast parallel mass-spectrometric approaches for the detection of the virus in the nasopharyngeal mucosa, saliva, sputum and other physiological fluids. Note: samples containing minor contamination of synthetic S peptides
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_05:10:54.491.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterAlexander Brzhozovskiy
SpeciesList scientific name: Severe acute respiratory syndrome coronavirus 2; NCBI TaxID: 2697049;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumenttimsTOF Pro
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-06-08 07:09:49ID requested
12020-08-13 22:25:47announced
22024-10-22 05:10:59announced2024-10-22: Updated project metadata.
Publication List
10.1021/acs.jproteome.0c00412;
Nikolaev EN, Indeykina MI, Brzhozovskiy AG, Bugrova AE, Kononikhin AS, Starodubtseva NL, Petrotchenko EV, Kovalev GI, Borchers CH, Sukhikh GT, Mass-Spectrometric Detection of SARS-CoV-2 Virus in Scrapings of the Epithelium of the Nasopharynx of Infected Patients via Nucleocapsid N Protein. J Proteome Res, 19(11):4393-4397(2020) [pubmed]
Keyword List
ProteomeXchange project tag: Sars-cov-2, Covid-19
submitter keyword: COVID,COVID-19,proteomics, SARS-COV-2
Contact List
Alexey Kononikhin
contact affiliationSkolkovo institute of science and technology
contact emailA.Kononikhin@skoltech.ru
lab head
Alexander Brzhozovskiy
contact affiliationV.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
contact emailagb.imbp@gmail.com
dataset submitter
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Dataset FTP location
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