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PXD026366 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleRapid and Sensitive Detection of SARS-CoV-2 Infection Using Quantitative Peptide Enrichment Analysis
DescriptionReliable, 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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterAndreas Hober
SpeciesList scientific name: Severe acute respiratory syndrome coronavirus 2; NCBI TaxID: 2697049; scientific name: Homo sapiens; NCBI TaxID: 9606;
InstrumentXevo TQ-XS
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-05-31 06:43:27ID requested
12021-11-15 10:00:38announced
Publication List
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]
Keyword List
submitter keyword: LC-MS, MRM, SARS-Cov-2, NCAP, RT-PCR, digest, peptide, SISCAPA, affinity
Contact List
Fredrik Edfors
contact affiliationScience for Life Laboratory, Department of Protein Science (KTH), Stockholm, Sweden
contact emailfredrik.edfors@scilifelab.se
lab head
Andreas Hober
contact affiliationScience for Life Laboratory, Department of Protein Science (KTH), Stockholm, Sweden
contact emailandreas.hober@scilifelab.se
dataset submitter
Full Dataset Link List
Panorama Public dataset URI