{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T05:10:08Z","timestamp":1790745008284,"version":"4.1.0"},"reference-count":38,"publisher":"American Chemical Society (ACS)","issue":"11","license":[{"start":{"date-parts":[[2020,7,22]],"date-time":"2020-07-22T00:00:00Z","timestamp":1595376000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-001"},{"start":{"date-parts":[[2020,7,22]],"date-time":"2020-07-22T00:00:00Z","timestamp":1595376000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-009"},{"start":{"date-parts":[[2020,7,22]],"date-time":"2020-07-22T00:00:00Z","timestamp":1595376000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-17-CE18-454 0023-01"],"award-info":[{"award-number":["ANR-17-CE18-454 0023-01"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["653316"],"award-info":[{"award-number":["653316"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006489","name":"Commissariat ? l'?nergie Atomique et aux ?nergies Alternatives","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006489","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,11,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Rapid but yet sensitive, specific, and high-throughput detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is key to diagnose infected people and to better control the spread of the virus. Alternative methodologies to PCR and immunodiagnostics that would not require specific reagents are worthy to investigate not only for fighting the COVID-19 pandemic but also to detect other emergent pathogenic threats. Here, we propose the use of tandem mass spectrometry to detect SARS-CoV-2 marker peptides in nasopharyngeal swabs. We documented that the signal from the microbiota present in such samples is low and can be overlooked when interpreting shotgun proteomic data acquired on a restricted window of the peptidome landscape. In this proof-of-concept study, simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC\u2013MS\/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. We argue that peptides ADETQALPQR and GFYAQGSR from the nucleocapsid protein are of utmost interest as their signal is intense and their elution can be obtained within a 3 min window in the tested conditions. These results pave the way for the development of time-efficient viral diagnostic tests based on mass spectrometry.<\/jats:p>","DOI":"10.1021\/acs.jproteome.0c00535","type":"journal-article","created":{"date-parts":[[2020,7,22]],"date-time":"2020-07-22T11:38:57Z","timestamp":1595417937000},"page":"4407-4416","source":"Crossref","is-referenced-by-count":94,"title":["Proteotyping SARS-CoV\u20112\nVirus from Nasopharyngeal\nSwabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window"],"prefix":"10.1021","volume":"19","author":[{"given":"Duarte","family":"Gouveia","sequence":"first","affiliation":[{"name":"Universite\u0301 Paris Saclay, CEA , , ,","place":["Bagnols-sur-Ce\u0300ze, France, 30200"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guylaine","family":"Miotello","sequence":"additional","affiliation":[{"name":"Universite\u0301 Paris Saclay, CEA , , ,","place":["Bagnols-sur-Ce\u0300ze, France, 30200"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabrice","family":"Gallais","sequence":"additional","affiliation":[{"name":"Universite\u0301 Paris Saclay, CEA , , ,","place":["Bagnols-sur-Ce\u0300ze, France, 30200"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Charles","family":"Gaillard","sequence":"additional","affiliation":[{"name":"Universite\u0301 Paris Saclay, CEA , , ,","place":["Bagnols-sur-Ce\u0300ze, France, 30200"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ste\u0301phanie","family":"Debroas","sequence":"additional","affiliation":[{"name":"Universite\u0301 Paris Saclay, CEA , , ,","place":["Bagnols-sur-Ce\u0300ze, France, 30200"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurent","family":"Bellanger","sequence":"additional","affiliation":[{"name":"Universite\u0301 Paris Saclay, CEA , , ,","place":["Bagnols-sur-Ce\u0300ze, France, 30200"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Philippe","family":"Lavigne","sequence":"additional","affiliation":[{"name":"Universite\u0301 Montpellier , , ,","place":["Montpellier, France"]},{"name":"CHU Ni\u0302mes , , ,","place":["Ni\u0302mes, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Albert","family":"Sotto","sequence":"additional","affiliation":[{"name":"CHU Ni\u0302mes , , ,","place":["Ni\u0302mes, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucia","family":"Grenga","sequence":"additional","affiliation":[{"name":"Universite\u0301 Paris Saclay, CEA , , ,","place":["Bagnols-sur-Ce\u0300ze, France, 30200"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Pible","sequence":"additional","affiliation":[{"name":"Universite\u0301 Paris Saclay, CEA , , ,","place":["Bagnols-sur-Ce\u0300ze, France, 30200"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1589-445X","authenticated-orcid":true,"given":"Jean","family":"Armengaud","sequence":"additional","affiliation":[{"name":"Universite\u0301 Paris Saclay, CEA , , ,","place":["Bagnols-sur-Ce\u0300ze, France, 30200"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2020,7,22]]},"reference":[{"issue":"7798","key":"2026081714255510000_cit1","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","article-title":"A pneumonia outbreak\nassociated with a new coronavirus of probable bat origin","volume":"579","author":"Zhou","year":"2020","journal-title":"Nature"},{"issue":"6","key":"2026081714255510000_cit2","doi-asserted-by":"publisher","first-page":"1997","DOI":"10.1111\/1462-2920.15039","article-title":"The importance of naturally attenuated\nSARS-CoV-2in\nthe fight against COVID-19","volume":"22","author":"Armengaud","year":"2020","journal-title":"Environ. Microbiol."},{"key":"2026081714255510000_cit3","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.202000107","article-title":"Shortlisting SARS-CoV-2 Peptides\nfor Targeted Studies from Experimental Data-Dependent Acquisition\nTandem Mass Spectrometry Data","volume":"20","author":"Gouveia","year":"2020","journal-title":"Proteomics"},{"key":"2026081714255510000_cit4","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.0c00280","article-title":"Mass spectrometric identifcation\nof SARS-CoV-2 proteins from gargle solution samples of COVID-19 patients","author":"Ihling","year":"2020","journal-title":"J. Proteome Res."},{"key":"2026081714255510000_cit5","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.25727","article-title":"Development and\nclinical application\nof a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection\ndiagnosis","author":"Li","year":"2020","journal-title":"J. Med. Virol."},{"issue":"4","key":"2026081714255510000_cit6","doi-asserted-by":"publisher","first-page":"5135","DOI":"10.1021\/acsnano.0c02823","article-title":"Rapid Detection\nof COVID-19 Causative Virus (SARS-CoV-2)\nin Human Nasopharyngeal Swab Specimens Using Field-Effect Transistor-Based\nBiosensor","volume":"14","author":"Seo","year":"2020","journal-title":"ACS Nano"},{"key":"2026081714255510000_cit7","doi-asserted-by":"publisher","DOI":"10.1001\/jama.2020.3786","article-title":"Detection\nof SARS-CoV-2 in Different Types of Clinical Specimens","author":"Wang","year":"2020","journal-title":"JAMA"},{"key":"2026081714255510000_cit8","doi-asserted-by":"publisher","first-page":"771","DOI":"10.1261\/rna.076232.120","article-title":"Overcoming the bottleneck to widespread testing: A rapid review of\nnucleic acid testing approaches for COVID-19 detection","volume":"26","author":"Esbin","year":"2020","journal-title":"RNA"},{"key":"2026081714255510000_cit9","doi-asserted-by":"publisher","first-page":"200642","DOI":"10.1148\/radiol.2020200642","article-title":"Correlation of Chest\nCT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China:\nA Report of 1014 Cases","volume":"296","author":"Ai","year":"2020","journal-title":"Radiology"},{"key":"2026081714255510000_cit10","doi-asserted-by":"publisher","first-page":"200343","DOI":"10.1148\/radiol.2020200343","article-title":"Chest CT for Typical\n2019-nCoV Pneumonia: Relationship to Negative\nRT-PCR Testing","volume":"296","author":"Xie","year":"2020","journal-title":"Radiology"},{"issue":"4","key":"2026081714255510000_cit11","doi-asserted-by":"publisher","first-page":"3822","DOI":"10.1021\/acsnano.0c02624","article-title":"Diagnosing COVID-19:\nThe Disease\nand Tools for Detection","volume":"14","author":"Udugama","year":"2020","journal-title":"ACS Nano"},{"key":"2026081714255510000_cit12","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.clinms.2019.04.004","article-title":"Pathogen proteotyping: a rapidly\ndeveloping application of mass spectrometry to address clinical concerns","volume":"14","author":"Grenga","year":"2019","journal-title":"Clinical Mass Spectrometry"},{"issue":"22","key":"2026081714255510000_cit13","doi-asserted-by":"publisher","first-page":"8584","DOI":"10.1039\/c3cs60081e","article-title":"Proteotyping\nfor the rapid identification of influenza virus and other biopathogens","volume":"42","author":"Downard","year":"2013","journal-title":"Chem. Soc. Rev."},{"issue":"4","key":"2026081714255510000_cit14","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1016\/j.syapm.2015.03.006","article-title":"Proteotyping: Proteomic characterization,\nclassification and identification of microorganisms--A prospectus","volume":"38","author":"Karlsson","year":"2015","journal-title":"Syst. Appl. Microbiol."},{"key":"2026081714255510000_cit15","doi-asserted-by":"publisher","first-page":"36082","DOI":"10.1038\/srep36082","article-title":"Identification\nof different respiratory viruses, after a cell culture step, by matrix\nassisted laser desorption\/ionization time of flight mass spectrometry\n(MALDI-TOF MS)","volume":"6","author":"Calderaro","year":"2016","journal-title":"Sci. Rep."},{"issue":"9","key":"2026081714255510000_cit16","doi-asserted-by":"publisher","first-page":"4088","DOI":"10.1021\/ac4040778","article-title":"Quantification\nof viral proteins of the avian H7 subtype of influenza virus: an isotope\ndilution mass spectrometry method applicable for producing more rapid\nvaccines in the case of an influenza pandemic","volume":"86","author":"Santana","year":"2014","journal-title":"Anal. 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Biol."},{"issue":"10","key":"2026081714255510000_cit26","doi-asserted-by":"publisher","first-page":"1555","DOI":"10.1080\/17435390.2016.1244299","article-title":"RNA-binding proteins\nare a major target of silica nanoparticles\nin cell extracts","volume":"10","author":"Klein","year":"2016","journal-title":"Nanotoxicology"},{"issue":"8","key":"2026081714255510000_cit27","doi-asserted-by":"publisher","first-page":"1437","DOI":"10.1002\/pmic.201400361","article-title":"The Unipept metaproteomics analysis pipeline","volume":"15","author":"Mesuere","year":"2015","journal-title":"Proteomics"},{"issue":"7","key":"2026081714255510000_cit28","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1093\/bioinformatics\/btq054","article-title":"Skyline: an open source document editor for creating\nand analyzing targeted proteomics experiments","volume":"26","author":"MacLean","year":"2010","journal-title":"Bioinformatics"},{"issue":"12","key":"2026081714255510000_cit29","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0082981","article-title":"Evaluating\nthe impact of different sequence databases on metaproteome analysis:\ninsights from a lab-assembled microbial mixture","volume":"8","author":"Tanca","year":"2013","journal-title":"PLoS One"},{"issue":"5","key":"2026081714255510000_cit30","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0010598","article-title":"The human nasal microbiota and Staphylococcus\naureus\ncarriage","volume":"5","author":"Frank","year":"2010","journal-title":"PLoS One"},{"key":"2026081714255510000_cit31","doi-asserted-by":"publisher","first-page":"1985","DOI":"10.3389\/fmicb.2019.01985","article-title":"Evaluation\nof Sample Preparation Methods for Fast Proteotyping\nof Microorganisms by Tandem Mass Spectrometry","volume":"10","author":"Hayoun","year":"2019","journal-title":"Front. Microbiol."},{"issue":"1","key":"2026081714255510000_cit32","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20199111","article-title":"Automated\nsample preparation with SP3 for low-input\nclinical proteomics","volume":"16","author":"Muller","year":"2020","journal-title":"Mol. Syst. Biol."},{"issue":"3","key":"2026081714255510000_cit33","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1002\/jms.3747","article-title":"Mass spectrometry for\nthe detection of bioterrorism agents: from environmental to clinical\napplications","volume":"51","author":"Duriez","year":"2016","journal-title":"J. Mass Spectrom."},{"issue":"2","key":"2026081714255510000_cit34","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1515\/cclm-2012-0291","article-title":"Mass spectrometry:\na revolution in clinical microbiology?","volume":"51","author":"Lavigne","year":"2013","journal-title":"Clin.\nChem. Lab. Med."},{"key":"2026081714255510000_cit35","doi-asserted-by":"publisher","first-page":"103887","DOI":"10.1016\/j.jprot.2020.103887","article-title":"High-throughput proteotyping of bacterial isolates\nby double barrel chromatography-tandem mass spectrometry based on\nmicroplate paramagnetic beads and phylopeptidomics","volume":"226","author":"Hayoun","year":"2020","journal-title":"J. Proteomics"},{"issue":"6","key":"2026081714255510000_cit36","doi-asserted-by":"publisher","first-page":"1059","DOI":"10.1007\/s10096-020-03913-9","article-title":"Viral RNA\nload as determined by cell culture as a management tool for discharge\nof SARS-CoV-2 patients from infectious disease wards","volume":"39","author":"La\nScola","year":"2020","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"2026081714255510000_cit37","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.3389\/fmicb.2019.01077","article-title":"Detection of Influenza\na Virus in Swine Nasal Swab Samples With a Wash-Free Magnetic Bioassay\nand a Handheld Giant Magnetoresistance Sensing System","volume":"10","author":"Su","year":"2019","journal-title":"Front. Microbiol."},{"key":"2026081714255510000_cit38","doi-asserted-by":"publisher","DOI":"10.1101\/2020.06.22.20136309","article-title":"Test sensitivity is secondary to frequency\nand turnaround time for COVID-19 surveillance","author":"Larremore","year":"2020","journal-title":"medRxiv"}],"container-title":["Journal of Proteome Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jproteome.0c00535","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jprobs\/article-pdf\/19\/11\/4407\/14425080\/pr0c00535.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jprobs\/article-pdf\/19\/11\/4407\/14425080\/pr0c00535.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T19:05:17Z","timestamp":1786993517000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jprobs\/article\/19\/11\/4407\/1383734\/Proteotyping-SARS-CoV-2-Virus-from-Nasopharyngeal"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,7,22]]},"references-count":38,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2020,7,22]]},"published-print":{"date-parts":[[2020,11,6]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jproteome.0c00535","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.06.19.161000","asserted-by":"object"}]},"ISSN":["1535-3893","1535-3907"],"issn-type":[{"value":"1535-3893","type":"print"},{"value":"1535-3907","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,7,22]]}}}