PXD026366

PXD026366 is an original dataset announced via ProteomeXchange.

Title	Rapid and Sensitive Detection of SARS-CoV-2 Infection Using Quantitative Peptide Enrichment Analysis
Description	Reliable, robust, large-scale molecular testing for SARS-CoV-2 is essential for monitoring the ongoing Covid-19 pandemic. We have developed a scalable analytical approach to detect viral proteins based on peptide immunoaffinity enrichment combined with liquid chromatography - mass spectrometry (LC-MS). This is a multiplexed strategy, based on targeted proteomics analysis and read-out by LC-MS, capable of precisely quantifying and confirming the presence of SARS-CoV-2 in PBS swab media from combined throat/nasopharynx/saliva samples. The results reveal that the levels of SARS-CoV-2 measured by LC-MS correlate well with their corresponding RT-PCR readout. The analytical workflow shows similar turnaround times as regular RT-PCR instrumentation with quantitative readout of viral proteins corresponding to cycle thresholds (Ct) equivalents ranging from 20 to 35. Using RT-PCR as a reference, we demonstrate that the LC-MS-based method has 100% specificity and 86% sensitivity when analyzing clinical samples collected from asymptomatic patients. These results suggest that a scalable analytical method based on LC-MS has a place in future pandemic preparedness centers to complement current virus detection technologies.
HostingRepository	PanoramaPublic
AnnounceDate	2021-11-15
AnnouncementXML	Submission_2021-11-15_10:00:37.972.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Andreas Hober
SpeciesList	scientific name: Severe acute respiratory syndrome coronavirus 2; NCBI TaxID: 2697049; scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Label:13C(6)15N(4)
Instrument	Xevo TQ-XS

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-31 06:43:27	ID requested
⏵ 1	2021-11-15 10:00:38	announced

Hober A, Tran-Minh KH, Foley D, McDonald T, Vissers JP, Pattison R, Ferries S, Hermansson S, Betner I, Uhlén M, Razavi M, Yip R, Pope ME, Pearson TW, Andersson LN, Bartlett A, Calton L, Alm JJ, Engstrand L, Edfors F, Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis. Elife, 10():(2021) [pubmed]

submitter keyword: LC-MS, MRM, SARS-Cov-2, NCAP, RT-PCR, digest, peptide, SISCAPA, affinity

Fredrik Edfors
contact affiliation	Science for Life Laboratory, Department of Protein Science (KTH), Stockholm, Sweden
contact email	fredrik.edfors@scilifelab.se
lab head
Andreas Hober
contact affiliation	Science for Life Laboratory, Department of Protein Science (KTH), Stockholm, Sweden
contact email	andreas.hober@scilifelab.se
dataset submitter

Panorama Public dataset URI