PXD026366-1

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, Uhl, é, n 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