PXD033790-1

PXD033790 is an original dataset announced via ProteomeXchange.

Title	SARS-CoV-2 PRM-MS Assay with Clinical Patient Samples
Description	The on-going SARS-CoV-2 (COVID-19) pandemic has called for an urgent need for rapid and high-throughput methods for mass testing for early detection, prevention and surveillance of the disease. We investigated whether targeted parallel reaction monitoring (PRM) quantification using high resolution Orbitrap instruments can provide the sensitivity and speed required for a high-throughput method that could be used for clinical diagnosis. We developed a high-throughput and sensitive PRM-MS assay that enables absolute quantification of SARS-CoV-2 nucleocapsid peptides with short turn-around times by using isotopically labelled synthetic SARS-CoV-2 concatenated peptides. We established a fast and high-throughput S-trap-based sample preparation method, which was then utilized for testing 25 positive and 25 negative heat-inactivated nasopharyngeal swab samples for SARS-CoV-2 detection. The method was able to differentiate between negative and some of the positive patients with high viral load .Moreover, based on the absolute quantification calculations, our data show that patients with Ct values as low as 17.5 correspond to NCAP protein amounts of around 7.5 pmol in swab samples. The present high-throughput method could potentially be utilized in specialized clinics as an alternative tool for detection of SARS-CoV-2 but will require enrichment of viral proteins in order to compete with RT-qPCR.
HostingRepository	PanoramaPublic
AnnounceDate	2022-06-24
AnnouncementXML	Submission_2022-06-24_10:07:24.250.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Atakan Arda Nalbant
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Label:15N(1); Label:15N(2); Label:15N(4)
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-09 21:51:34	ID requested
⏵ 1	2022-06-24 10:07:24	announced

Gajbhiye A, Nalbant A, Heunis T, Sidgwick F, Porter A, Taha Y, Trost M, A fast and sensitive absolute quantification assay for the detection of SARS-CoV-2 peptides using parallel reaction monitoring mass spectrometry. J Proteomics, 265():104664(2022) [pubmed]

submitter keyword: COVID-19, SARS-CoV-2, Proteomics, PRM, LC-MS, mass spectrometry, parallel reaction monitoring

Matthias Trost
contact affiliation	Newcastle University
contact email	matthias.trost@newcastle.ac.uk
lab head
Atakan Arda Nalbant
contact affiliation	Newcastle University
contact email	atakan.nalbant@newcastle.ac.uk
dataset submitter

Panorama Public dataset URI