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We have developed a scalable analytical approach to detect viral proteins based on peptide immuno-affinity 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 phosphate-buffered saline (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 correspondingreal-time polymerase chain reaction (RT-PCR) read-out (r = 0.79). The analytical workflow shows similar turnaround times as regular RT-PCR instrumentation with a quantitative read-out of viral proteins corresponding to cycle thresholds (Ct) equivalents ranging from 21 to 34. Using RT-PCR as a reference, we demonstrate that the LC-MS-based method has 100% negative percent agreement (estimated specificity) and 95% positive percent agreement (estimated sensitivity) when analyzing clinical samples collected from asymptomatic individuals with a Ct within the limit of detection of the mass spectrometer (Ct \u2264 30). 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.<\/jats:p>","DOI":"10.7554\/elife.70843","type":"journal-article","created":{"date-parts":[[2021,11,4]],"date-time":"2021-11-04T15:15:13Z","timestamp":1636038913000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.70843","source":"Crossref","is-referenced-by-count":28,"title":["Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis"],"prefix":"10.7554","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8947-2562","authenticated-orcid":true,"given":"Andreas","family":"Hober","sequence":"first","affiliation":[{"name":"Science for Life Laboratory","place":["Solna, Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khue Hua","family":"Tran-Minh","sequence":"additional","affiliation":[{"name":"Science for Life 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