{"database":"panorama","file_versions":[],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["Valdemir Carvalho"],"species":["Severe Acute Respiratory Syndrome Coronavirus 2"],"full_dataset_link":["https://panoramaweb.org/Fleury_SARS-CoV-2.url"],"submitter_email":["melechco@gmail.com"],"submitter_affiliation":["Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil"],"sample_protocol":[""],"repository":["PanoramaPublic"],"data_protocol":[""],"pubmed_abstract":["The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. Here, we develop a high-throughput targeted proteomics assay to detect SARS-CoV-2 nucleoprotein peptides directly from nasopharyngeal and oropharyngeal swabs. A modified magnetic particle-based proteomics approach implemented on a robotic liquid handler enables fully automated preparation of 96 samples within 4 hours. A TFC-MS system allows multiplexed analysis of 4 samples within 10 min, enabling the processing of more than 500 samples per day. We validate this method qualitatively (Tier 3) and quantitatively (Tier 1) using 985 specimens previously analyzed by real-time RT-PCR, and detect up to 84% of the positive cases with up to 97% specificity. The presented strategy has high sample stability and should be considered as an option for SARS-CoV-2 testing in large populations."],"pubmed_title":["Establishing a mass spectrometry-based system for rapid detection of SARS-CoV-2 in large clinical sample cohorts."],"pubmed_authors":["Cardozo Karina Helena Morais KHM, Lebkuchen Adriana A, Okai Guilherme Gonçalves GG, Schuch Rodrigo Andrade RA, Viana Luciana Godoy LG, Olive Aline Nogueira AN, Lazari Carolina Dos Santos CDS, Fraga Ana Maria AM, Granato Celso Francisco Hernandes CFH, Pintão Maria Carolina Tostes MCT, Carvalho Valdemir Melechco VM"],"pubmed_abstract_synonyms":["COVID19, other disease, GRP1/cytohesin 1, Procedures, determination, Peptidomics, Effects, acetylglucosaminyltransferase-like protein, COVID-19, Mbp1, 2019 novel coronavirus, RT-PCR, SARS CoV 2 Virus, LARGE1, dIKK-gamma, COVID19 Virus, froggy, prevention, Long Term, Gyltl1a, CG11633, cytohesin/GRP1, School-Age, Polypeptides, method, Techniques, Tier, peptido, SARS, diseases, Gyltl1a., Method, DmIKK-gamma, GRP1, method used in an experiment, Grp1, Novel Coronavirus, Virus, Studies, disease or disorder, diseases and disorders, β-coronavirus, dmIKKgamma, IKK[[gamma]], myd, prevention and control, Effect, 2019-nCoV, Technique, IKKg, KEY, Key, 2019 Novel Coronaviruses, School-Age Populations, SARS Coronavirus 2, human disease, β-CoVs, anatomical systems, Viruses, like-acetylglucosaminyltransferase, reference sample, peptides, Longterm, MDDGB6, PTPSTEP, Wuhan Seafood Market Pneumonia Virus, l(2)SH2 0323, Mbp-1, severe acute respiratory syndrome coronavirus 2, LARGE, metazoa, Long-Term, Population, beta-CoVs, Community Health, non-neoplastic, preventive measures, Study, BPFD#36, COVID-19 Virus, Neural-specific protein-tyrosine phosphatase, IKK, Methodological Studies, scientific observation, l(2)k08110, sample, disorder, Homo sapiens disease, peptidos, Long-Term Effect, School Age Population, Long-Term Effects, Wuhan Coronavirus, GPH, Controlled, measuring, Controlling, SARS-CoV-2 Viruses, preventive therapy, β-CoV, 2019 Novel Coronavirus, beta-CoV, gyltl1b-b, COVID-19 Viruses, animalia, disorders, SARS-CoV-2, Longterm Effect, stepk, Coronavirus 2, medical condition, Procedure, Peptide, IKKgamma, COVID19 Viruses, DmIKKgamma, Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2 Virus, Public, dIKK, MDDGA6, School Age, liquid_handling_instrument, mKIAA0609, chemical analysis, Long Term Effects, Kenny, 3.1.3.48, Diseases, condition, Coronavirus, liquid_handler, Environment, KIAA0609, l(2)SH0323, acetylglucosaminyltransferase-like 1A, CYH1, fg, Populations, 2019 Novel, betacoronavirus, gyltl1b, Pandemic, Nucleoprotein, Step, CG11628, Dmikkgamma, Coronavirus Disease 2019 Virus, prophylaxis, mdc1d, IKK-gamma, Magnetic, Striatum-enriched protein-tyrosine phosphatase, Wuhan, Methodological, CG16910, LARGE_HUMAN, Methodological Study, School Age Populations, sample population, SARS-coronavirus 2, DmelCG11628, Longterm Effects, plan specification, MDC1D, disease, Health, DmelCG16910, like-glycosyltransferase, enr, STEP, control, 2019, Preventive Medicine & Public Health, Peptid, COVID 19 Virus, School-Age Population, assay, Polypeptide, Preventive Medicine and Public Health, reverse transcription polymerase chain reaction, Community, glycosyltransferase-like protein LARGE1"],"name_synonyms":["FBgn0003149, COVID19, SPS1., SARS-CoV-2 Viruses, 2019 Novel Coronavirus, β-CoV, beta-CoV, SRML1, COVID-19 Viruses, DmelCG5939, COVID-19, PAPT, SARS-CoV-2, 2019 novel coronavirus, Coronavirus 2, SARS CoV 2 Virus, SPDSY, COVID19 Virus, Multiple Reaction Monitoring, COVID19 Viruses, Para, Severe Acute Respiratory Syndrome Coronavirus 2, SARS, prm, SARS-CoV-2 Virus, mPM, Novel Coronavirus, Virus, Coronavirus, l(3)S010605, β-coronavirus, CG5939, 2019-nCoV, 2019 Novel Coronaviruses, SARS Coronavirus 2, β-CoVs, 2019 Novel, betacoronavirus, Viruses, MRM, 0106/05, Coronavirus Disease 2019 Virus, PM/mPM, Wuhan Seafood Market Pneumonia Virus, severe acute respiratory syndrome coronavirus 2, Wuhan, beta-CoVs, SARS-coronavirus 2, COVID-19 Virus, l(3)10631, 2019, COVID 19 Virus, Wuhan Coronavirus, pm, PM"],"description_synonyms":["determination, acetylglucosaminyltransferase-like protein, Mbp1, SARS-CoV infection, 2019 novel coronavirus, RT-PCR, SARS ASSOC CORONAVIRUS, prevention, Long Term, School-Age, Polypeptides, Techniques, Tier, peptido, diseases, Gyltl1a., Coronaviruses, Method, GRP1, Grp1, Novel Coronavirus, Rabbit Coronavirus, Virus, diseases and disorders, Min, Analysis, myd, prevention and control, Effect, IKKg, DmelCG42273, KEY, Key, Mass Spectrum Analysis, human disease, like-acetylglucosaminyltransferase, reference sample, peptides, Analyses, PTPSTEP, min, Mbp-1, mAPC, beta-CoVs, Community Health, AI047805, preventive measures, SARS coronavirus disease or disorder, Methodological Studies, scientific observation, l(2)k08110, sample, Homo sapiens disease, SARS (Severe Acute Respiratory Syndrome), Respiratory Syndrome, Long-Term Effects, GPH, SARS-CoV-2 Viruses, preventive therapy, β-CoV, SARS coronavirus caused disease or disorder, gyltl1b-b, COVID-19 Viruses, animalia, SARS-CoV-2, Dmel_CG7826, Longterm Effect, Coronavirus 2, Procedure, Spectrum Analysis, Spectroscopy, COVID19 Viruses, DmIKKgamma, Dm1, SARS-CoV-2 Virus, dIKK, MDDGA6, School Age, mKIAA0609, Kenny, 3.1.3.48, Diseases, Severe acute respiratory syndrome (disorder), Coronavirus, liquid_handler, KIAA0609, acetylglucosaminyltransferase-like 1A, Dmel_CG7835, Severe Acute, Mnb, MNB, fg, Populations, gyltl1b, Pandemic, Step, CG11628, Coronavirus Disease 2019 Virus, mdc1d, IKK-gamma, Spectrometry, Striatum-enriched protein-tyrosine phosphatase, Methodological, AW124434, LARGE_HUMAN, Methodological Study, MDC1D, disease, Health, DmelCG16910, acute respiratory coronavirus infection, enr, STEP, 2019, Preventive Medicine & Public Health, School-Age Population, Polypeptide, Preventive Medicine and Public Health, Community, COVID19, other disease, GRP1/cytohesin 1, Procedures, Peptidomics, Effects, COVID-19, Gene, Spectrum Analyses, SARS CoV 2 Virus, LARGE1, dIKK-gamma, COVID19 Virus, froggy, CG7826, Gyltl1a, CG11633, cytohesin/GRP1, method, SARS, DmIKK-gamma, method used in an experiment, Gene Products, Mass, CG7835, Studies, disease or disorder, CG42273, β-coronavirus, dmIKKgamma, IKK[[gamma]], 2019-nCoV, Technique, Mass Spectroscopy, 2019 Novel Coronaviruses, School-Age Populations, SARS Coronavirus 2, β-CoVs, Rabbit, Viruses, Longterm, SARS coronavirus infectious disease, MDDGB6, Wuhan Seafood Market Pneumonia Virus, l(2)SH2 0323, severe acute respiratory syndrome coronavirus 2, LARGE, metazoa, Long-Term, Population, non-neoplastic, Study, BPFD#36, COVID-19 Virus, Neural-specific protein-tyrosine phosphatase, IKK, disorder, peptidos, Long-Term Effect, School Age Population, Chromatographies, Wuhan Coronavirus, Controlled, measuring, Controlling, DYRK1, 2019 Novel Coronavirus, beta-CoV, Rabbit Coronaviruses, Proteins, disorders, stepk, SARS-associated coronavirus, medical condition, Peptide, IKKgamma, Severe Acute Respiratory Syndrome Coronavirus 2, MS, Public, liquid_handling_instrument, chemical analysis, Protein, Long Term Effects, condition, Dyrk1, Environment, l(2)SH0323, Mass Spectrum Analyses, CYH1, AU020952, Mass Spectrum, 2019 Novel, betacoronavirus, Nucleoprotein, Dmikkgamma, prophylaxis, severe acute respiratory syndrome, CC1, Magnetic, Wuhan, CG16910, School Age Populations, sample population, SARS-coronavirus 2, DmelCG11628, Longterm Effects, ME-IV, Protein Gene Products, plan specification, Gene Proteins, Acute, like-glycosyltransferase, control, Peptid, COVID 19 Virus, assay, reverse transcription polymerase chain reaction, Severe, glycosyltransferase-like protein LARGE1"],"pubmed_title_synonyms":["COVID19, SARS-CoV-2 Viruses, 2019 Novel Coronavirus, β-CoV, beta-CoV, gyltl1b-b, COVID-19 Viruses, acetylglucosaminyltransferase-like protein, COVID-19, SARS-CoV-2, Mbp1, 2019 novel coronavirus, Coronavirus 2, Spectrum Analyses, SARS CoV 2 Virus, Spectrum Analysis, LARGE1, COVID19 Virus, froggy, Gyltl1a, Spectroscopy, COVID19 Viruses, MS, Severe Acute Respiratory Syndrome Coronavirus 2, SARS, SARS-CoV-2 Virus, MDDGA6, mKIAA0609, Novel Coronavirus, Mass, Virus, Coronavirus, Analysis, β-coronavirus, KIAA0609, myd, 2019-nCoV, Mass Spectrum Analyses, acetylglucosaminyltransferase-like 1A, Mass Spectroscopy, 2019 Novel Coronaviruses, Mass Spectrum Analysis, fg, Mass Spectrum, SARS Coronavirus 2, anatomical systems, β-CoVs, 2019 Novel, betacoronavirus, gyltl1b, Viruses, like-acetylglucosaminyltransferase, Analyses, Coronavirus Disease 2019 Virus, MDDGB6, Wuhan Seafood Market Pneumonia Virus, mdc1d, Spectrometry, Mbp-1, severe acute respiratory syndrome coronavirus 2, LARGE, Wuhan, beta-CoVs, LARGE_HUMAN, sample population, SARS-coronavirus 2, BPFD#36, COVID-19 Virus, MDC1D, sample., like-glycosyltransferase, enr, 2019, COVID 19 Virus, Wuhan Coronavirus, glycosyltransferase-like protein LARGE1"],"additional_accession":[]},"is_claimable":false,"name":"SARS-CoV-2_PRM_SRM_targeted_acquisitions","description":"The current outbreak of severe acute respiratory syndrome associated with coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. We developed a high-throughput targeted proteomics assay to detect SARS-CoV-2 proteins directly from nasopharyngeal and oropharyngeal swabs. Sample preparation was fully automated by using a modified magnetic particle-based proteomics approach implemented on a robotic liquid handler. The use of turbulent flow chromatography included four times multiplexed on-line sample cleanup and liquid chromatography separation. Mass spectrometry detection of nucleoprotein peptides was achieved within 2.5 min, enabling the analysis of more than 500 samples per day. The method was validated qualitatively (Tier 3) and quantitatively (Tier 1) using 855 specimens previously analyzed by real-time RT-PCR and was able to detect up to 84% of positive cases with up to 97% of specificity. The strategy here presented has high sample stability and should be considered as an option for testing in large populations.","dates":{"publication":"Mon Dec 07 00:00:00 GMT 2020"},"accession":"PXD019300","cross_references":{"TAXONOMY":["2697049"],"pubmed":["33273458"]}}