{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T21:02:16Z","timestamp":1787000536538,"version":"build-2736575974"},"reference-count":49,"publisher":"American Chemical Society (ACS)","issue":"50","license":[{"start":{"date-parts":[[2021,12,7]],"date-time":"2021-12-07T00:00:00Z","timestamp":1638835200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003852","name":"Regione Campania","doi-asserted-by":"publisher","award":["D64I200003800"],"award-info":[{"award-number":["D64I200003800"]}],"id":[{"id":"10.13039\/501100003852","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,21]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Numerous reverse transcription polymerase chain reaction (RT-PCR) tests have emerged over the past year as the gold standard for detecting millions of cases of SARS-CoV-2 reported daily worldwide. However, problems with critical shortages of key reagents such as PCR primers and RNA extraction kits and unpredictable test reliability related to high viral replication cycles have triggered the need for alternative methodologies to PCR to detect specific COVID-19 proteins. Several authors have developed methods based on liquid chromatography with tandem mass spectrometry (LC\u2013MS\/MS) to confirm the potential of the technique to detect two major proteins, the spike and the nucleoprotein, of COVID-19. In the present work, an S-Trap mini spin column digestion protocol was used for sample preparation prodromal to LC\u2013MS\/MS analysis in multiple reactions monitoring ion mode (MRM) to obtain a comprehensive method capable of detecting different viral proteins. The developed method was applied to n. 81 oro\/nasopharyngeal swabs submitted in parallel to quantitative reverse transcription PCR (RT-qPCR) assays to detect RdRP, the S and N genes specific for COVID-19, and the E gene for all Sarbecoviruses, including SARS-CoV-2 (with cycle negativity threshold set to 40). A total of 23 peptides representative of the six specific viral proteins were detected in the monitoring of 128 transitions found to have good ionic currents extracted in clinical samples that reacted differently to the PCR assay. The best instrumental response came from the FLPFQFGR sequence of spike [558\u2212566] peptide used to test the analytical performance of the method that has good sensitivity with a low false-negative rate. Transition monitoring using a targeted MS approach has the great potential to detect the fragmentation reactions of any peptide molecularly defined by a specific amino acid sequence, offering the extensibility of the approach to any viral sequence including derived variants and thus providing insights into the development of new types of clinical diagnostics.<\/jats:p>","DOI":"10.1021\/acsomega.1c05587","type":"journal-article","created":{"date-parts":[[2021,12,7]],"date-time":"2021-12-07T19:41:50Z","timestamp":1638906110000},"page":"34945-34953","source":"Crossref","is-referenced-by-count":19,"title":["Identification of SARS-CoV\u20112 Proteins from\nNasopharyngeal Swabs Probed by Multiple Reaction Monitoring Tandem\nMass Spectrometry"],"prefix":"10.1021","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9169-3452","authenticated-orcid":true,"given":"Gabriella","family":"Pinto","sequence":"first","affiliation":[{"name":"University of Naples Federico II , , Via Cinthia 26 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80145"]},{"name":"University of Naples Federico II , , Via Pansini 5 , ,","place":["Naples, Italy, 80145"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabrizio","family":"Quarantelli","sequence":"additional","affiliation":[{"name":"CEINGE Advanced Biotechnology , Via Gaetano Salvatore 486 , ,","place":["Naples, Italy, 80145"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolina","family":"Fontanarosa","sequence":"additional","affiliation":[{"name":"University of Naples Federico II , , Via Cinthia 26 , ,","place":["Naples, Italy, 80126"]},{"name":"Istituto Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario , Viale delle Medaglie d\u2019Oro, 305 , ,","place":["Rome, Italy, 00136"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberto","family":"Siciliano","sequence":"additional","affiliation":[{"name":"CEINGE Advanced Biotechnology , Via Gaetano Salvatore 486 , ,","place":["Naples, Italy, 80145"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carmela","family":"Di Domenico","sequence":"additional","affiliation":[{"name":"CEINGE Advanced Biotechnology , Via Gaetano Salvatore 486 , ,","place":["Naples, Italy, 80145"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barbara","family":"Izzo","sequence":"additional","affiliation":[{"name":"CEINGE Advanced Biotechnology , Via Gaetano Salvatore 486 , ,","place":["Naples, Italy, 80145"]},{"name":"University of Naples Federico II , , Via Pansini 5 , ,","place":["Naples, Italy, 80145"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Piero","family":"Pucci","sequence":"additional","affiliation":[{"name":"University of Naples Federico II , , Via Cinthia 26 , ,","place":["Naples, Italy, 80126"]},{"name":"CEINGE Advanced Biotechnology , Via Gaetano Salvatore 486 , ,","place":["Naples, Italy, 80145"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gennaro","family":"Marino","sequence":"additional","affiliation":[{"name":"University of Naples Federico II , , Via Cinthia 26 , ,","place":["Naples, Italy, 80126"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Massimo","family":"Zollo","sequence":"additional","affiliation":[{"name":"CEINGE Advanced Biotechnology , Via Gaetano Salvatore 486 , ,","place":["Naples, Italy, 80145"]},{"name":"University of Naples Federico II , , Via Pansini 5 , ,","place":["Naples, Italy, 80145"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angela","family":"Amoresano","sequence":"additional","affiliation":[{"name":"University of Naples Federico II , , Via Cinthia 26 , ,","place":["Naples, Italy, 80126"]},{"name":"Istituto Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario , Viale delle Medaglie d\u2019Oro, 305 , ,","place":["Rome, Italy, 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Mass Spectrom."},{"key":"2026081710241131100_cit16","volume-title":"Virus\nagainst Virus:\nA Potential Treatment for 2019-nCov (SARS-CoV-2) and other RNA Viruses","author":"Nguyen","year":"2020"},{"key":"2026081710241131100_cit17","doi-asserted-by":"publisher","first-page":"766","DOI":"10.1016\/j.cell.2016.06.041","article-title":"Human SRMAtlas: a resource\nof targeted assays to quantify\nthe complete human proteome","volume":"166","author":"Kusebauch","year":"2016","journal-title":"Cell"},{"key":"2026081710241131100_cit18","doi-asserted-by":"publisher","first-page":"4407","DOI":"10.1021\/acs.jproteome.0c00535","article-title":"Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs:\na proof-of-concept focused on a 3 min mass spectrometry window","volume":"19","author":"Gouveia","year":"2020","journal-title":"J. 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Proteome Res."},{"key":"2026081710241131100_cit26c","doi-asserted-by":"publisher","first-page":"4393","DOI":"10.1021\/acs.jproteome.0c00412","article-title":"Mass-Spectrometric\nDetection of SARS-CoV-2 Virus in Scrapings of the Epithelium of the\nNasopharynx of Infected Patients via Nucleocapsid N Protein","volume":"19","author":"Nikolaev","year":"2020","journal-title":"J. Proteome Res."},{"key":"2026081710241131100_cit26d","doi-asserted-by":"publisher","DOI":"10.1101\/2020.08.05.20168948","article-title":"Development of mass spectrometry-based targeted assay for direct\ndetection of novel SARS-CoV-2 coronavirus from clinical specimens","volume":"5","author":"Renuse","year":"2020","journal-title":"medRxiv"},{"key":"2026081710241131100_cit26e","doi-asserted-by":"publisher","first-page":"1503","DOI":"10.1074\/mcp.RA120.002164","article-title":"Data,\nreagents, assays and merits of proteomics for SARS-CoV-2 research\nand testing","volume":"19","author":"Zecha","year":"2020","journal-title":"Mol. Cell. Proteomics"},{"key":"2026081710241131100_cit27","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1007\/s42485-020-00044-9","article-title":"A rapid and sensitive\nmethod to detect SARS-CoV-2 virus using targeted-mass spectrometry","volume":"11","author":"Singh","year":"2020","journal-title":"J. Proteins Proteomics"},{"key":"2026081710241131100_cit28","doi-asserted-by":"publisher","DOI":"10.1101\/2020.11.18.20231688","article-title":"Cov-MS:\na community-based template assay for clinical MS-based protein detection\nin SARS-CoV-2 patients","author":"Van\nPuyvelde","year":"2020","journal-title":"medRxiv"},{"key":"2026081710241131100_cit29","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s41664-021-00197-6","article-title":"Mass Spectrometry-based\nProteomics and Glycoproteomics\nin COVID-19 Biomarkers Identification: A Mini-review","author":"Zhong","year":"2021","journal-title":"J. Anal. Test."},{"key":"2026081710241131100_cit30","doi-asserted-by":"publisher","DOI":"10.1016\/j.envpol.2020.115368","article-title":"Diurnal and temporal\nchanges in air pollution during\nCOVID-19 strict lockdown over different regions of India","volume":"266","author":"Singh","year":"2020","journal-title":"Environ. Pollut."},{"key":"2026081710241131100_cit31","doi-asserted-by":"publisher","DOI":"10.1101\/2020.04.23.057810","article-title":"Targeted proteomics\nas a tool to detect SARS-CoV-2 proteins in clinical specimens","author":"Bezstarosti","year":"2021","journal-title":"bioRxiv"},{"key":"2026081710241131100_cit32","doi-asserted-by":"publisher","first-page":"2013","DOI":"10.1021\/jasms.0c00238","article-title":"Mass Spectrometry\nTechniques in Emerging Pathogens\nStudies: COVID-19 Perspectives","volume":"31","author":"Mahmud","year":"2020","journal-title":"J. Am. Soc.\nMass Spectrom."},{"key":"2026081710241131100_cit33","doi-asserted-by":"publisher","first-page":"2974","DOI":"10.1021\/acsabm.1c00102","article-title":"SERS based lateral flow immunoassay\nfor point-of-care detection of SARS-CoV-2 in clinical samples","volume":"4","author":"Yadav","year":"2021","journal-title":"ACS Appl. Bio Mater."},{"key":"2026081710241131100_cit34","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2021.102322","article-title":"Common variants at 21q22. 3 locus\ninfluence MX1 gene expression and susceptibility to severe COVID-19","volume":"24","author":"Andolfo","year":"2020","journal-title":"iScience"},{"key":"2026081710241131100_cit35","doi-asserted-by":"publisher","DOI":"10.3390\/diagnostics11020288","article-title":"SARS-CoV-2\nSubgenomic\nN (sgN) Transcripts in Oro-Nasopharyngeal Swabs Correlate with the\nHighest Viral Load, as Evaluated by Five Different Molecular Methods","volume":"11","author":"Zollo","year":"2021","journal-title":"Diagnostics"}],"container-title":["ACS Omega"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acsomega.1c05587","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/acsodf\/article-pdf\/6\/50\/34945\/3670258\/ao1c05587.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/acsodf\/article-pdf\/6\/50\/34945\/3670258\/ao1c05587.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T14:46:57Z","timestamp":1786978017000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/acsodf\/article\/6\/50\/34945\/381224\/Identification-of-SARS-CoV-2-Proteins-from"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,12,7]]},"references-count":49,"journal-issue":{"issue":"50","published-online":{"date-parts":[[2021,12,7]]},"published-print":{"date-parts":[[2021,12,21]]}},"URL":"https:\/\/doi.org\/10.1021\/acsomega.1c05587","relation":{},"ISSN":["2470-1343"],"issn-type":[{"value":"2470-1343","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,12,7]]}}}