{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T12:31:41Z","timestamp":1784637101910,"version":"3.55.0"},"reference-count":65,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,5,10]],"date-time":"2021-05-10T00:00:00Z","timestamp":1620604800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,5,10]],"date-time":"2021-05-10T00:00:00Z","timestamp":1620604800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["1U24CA199347"],"award-info":[{"award-number":["1U24CA199347"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["T32GM008347"],"award-info":[{"award-number":["T32GM008347"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["031 A538A\/A538C RBC"],"award-info":[{"award-number":["031 A538A\/A538C RBC"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["031L0101B\/031L0101C de.NBI-epi"],"award-info":[{"award-number":["031L0101B\/031L0101C de.NBI-epi"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["031L0106 de.STAIR (de.NBI)"],"award-info":[{"award-number":["031L0106 de.STAIR (de.NBI)"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SFB 992\/1 2012"],"award-info":[{"award-number":["SFB 992\/1 2012"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Clin Proteom"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>In this study we have compiled a list of 636 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639-peptide possibilities to 87 peptides that were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Through stringent p-value cutoff combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from patient samples. We also contend that samples harvested from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12014-021-09321-1","type":"journal-article","created":{"date-parts":[[2021,5,10]],"date-time":"2021-05-10T06:04:29Z","timestamp":1620626669000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)"],"prefix":"10.1186","volume":"18","author":[{"given":"Andrew T.","family":"Rajczewski","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Subina","family":"Mehta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dinh Duy An","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bj\u00f6rn","family":"Gr\u00fcning","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James E.","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"McGowan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy J.","family":"Griffin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0984-0973","authenticated-orcid":false,"given":"Pratik D.","family":"Jagtap","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,5,10]]},"reference":[{"issue":"8","key":"9321_CR1","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1056\/NEJMoa2001017","volume":"382","author":"N Zhu","year":"2020","unstructured":"Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, Niu P, Zhan F, Ma X, Wang D, Xu W, Wu G, Gao GF, Tan W. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020;382(8):727\u201333.","journal-title":"N Engl J Med"},{"key":"9321_CR2","unstructured":"Nuzzo J, Moss W, Kahn J, Rutgow L et al. Have states flattened the curve? https:\/\/coronavirus.jhu.edu\/. Accessed 5 May 2021."},{"issue":"8","key":"9321_CR3","doi-asserted-by":"publisher","first-page":"1069","DOI":"10.1007\/s42399-020-00363-4","volume":"2","author":"A Sanyaolu","year":"2020","unstructured":"Sanyaolu A, Okorie C, Marinkovic A, Patidar R, Younis K, Desai P, Hosein Z, Padda I, Mangat J, Altaf M. Comorbidity and its impact on patients with COVID-19. SN Comprehens Clin Med. 2020;2(8):1069\u201376.","journal-title":"SN Comprehens Clin Med"},{"issue":"6","key":"9321_CR4","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1016\/j.jinf.2020.03.037","volume":"80","author":"Q Ye","year":"2020","unstructured":"Ye Q, Wang B, Mao J. The pathogenesis and treatment of the `Cytokine Storm\u2019 in COVID-19. J Infect. 2020;80(6):607\u201313.","journal-title":"J Infect"},{"issue":"19","key":"9321_CR5","doi-asserted-by":"publisher","first-page":"1813","DOI":"10.1056\/NEJMoa2007764","volume":"383","author":"JH Beigel","year":"2020","unstructured":"Beigel JH, Tomashek KM, Dodd LE, Mehta AK, Zingman BS, Kalil AC, Hohmann E, Chu HY, Luetkemeyer A, Kline S, de Lopez Castilla D, Finberg RW, Dierberg K, Tapson V, Hsieh L, Patterson TF, Paredes R, Sweeney DA, Short WR, Touloumi G, Lye DC, Ohmagari N, Oh MD, Ruiz-Palacios GM, Benfield T, F\u00e4tkenheuer G, Kortepeter MG, Atmar RL, Creech CB, Lundgren J, Babiker AG, Pett S, Neaton JD, Burgess TH, Bonnett T, Green M, Makowski M, Osinusi A, Nayak S, Lane HC. Remdesivir for the treatment of Covid-19\u2014final report. New Engl J Med. 2020;383(19):1813\u201326.","journal-title":"New Engl J Med."},{"issue":"7827","key":"9321_CR6","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1038\/s41586-020-2577-1","volume":"586","author":"L Riva","year":"2020","unstructured":"Riva L, Yuan S, Yin X, Martin-Sancho L, Matsunaga N, Pache L, Burgstaller-Muehlbacher S, De Jesus PD, Teriete P, Hull MV. Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing. Nature. 2020;586(7827):113\u20139.","journal-title":"Nature"},{"issue":"10","key":"9321_CR7","doi-asserted-by":"publisher","first-page":"2172","DOI":"10.1016\/j.mayocp.2020.07.021","volume":"95","author":"GA Poland","year":"2020","unstructured":"Poland GA, Ovsyannikova IG, Crooke SN, Kennedy RB. SARS-CoV-2 vaccine development: current status. Mayo Clin Proc. 2020;95(10):2172\u201388.","journal-title":"Mayo Clin Proc"},{"key":"9321_CR8","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2020.08.002","author":"G Dagotto","year":"2020","unstructured":"Dagotto G, Yu J, Barouch DH. Approaches and challenges in SARS-CoV-2 vaccine development. Cell Host Microbe. 2020. https:\/\/doi.org\/10.1016\/j.chom.2020.08.002.","journal-title":"Cell Host Microbe"},{"issue":"20","key":"9321_CR9","doi-asserted-by":"publisher","first-page":"1920","DOI":"10.1056\/NEJMoa2022483","volume":"383","author":"LA Jackson","year":"2020","unstructured":"Jackson LA, Anderson EJ, Rouphael NG, Roberts PC, Makhene M, Coler RN, McCullough MP, Chappell JD, Denison MR, Stevens LJ, Pruijssers AJ, McDermott A, Flach B, Doria-Rose NA, Corbett KS, Morabito KM, O\u2019Dell S, Schmidt SD, Swanson PA, Padilla M, Mascola JR, Neuzil KM, Bennett H, Sun W, Peters E, Makowski M, Albert J, Cross K, Buchanan W, Pikaart-Tautges R, Ledgerwood JE, Graham BS, Beigel JH. An mRNA vaccine against SARS-CoV-2\u2014preliminary report. N Engl J Med. 2020;383(20):1920\u201331.","journal-title":"N Engl J Med"},{"issue":"9","key":"9321_CR10","doi-asserted-by":"publisher","first-page":"e01438","DOI":"10.1128\/JCM.01438-20","volume":"58","author":"M Nagura-Ikeda","year":"2020","unstructured":"Nagura-Ikeda M, Imai K, Tabata S, Miyoshi K, Murahara N, Mizuno T, Horiuchi M, Kato K, Imoto Y, Iwata M, Mimura S, Ito T, Tamura K, Kato Y. Clinical evaluation of self-collected saliva by quantitative reverse transcription-PCR (RT-qPCR), Direct RT-qPCR, reverse transcription\u2013loop-mediated isothermal amplification, and a rapid antigen test to diagnose COVID-19. J Clin Microbiol. 2020;58(9):e01438-e1520.","journal-title":"J Clin Microbiol"},{"issue":"3","key":"9321_CR11","doi-asserted-by":"publisher","first-page":"2000045","DOI":"10.2807\/1560-7917.ES.2020.25.3.2000045","volume":"25","author":"VM Corman","year":"2020","unstructured":"Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, Bleicker T, Br\u00fcnink S, Schneider J, Schmidt ML, Mulders DG, Haagmans BL, van der Veer B, van den Brink S, Wijsman L, Goderski G, Romette J-L, Ellis J, Zambon M, Peiris M, Goossens H, Reusken C, Koopmans MP, Drosten C. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance. 2020;25(3):2000045.","journal-title":"Eurosurveillance"},{"issue":"8","key":"9321_CR12","doi-asserted-by":"publisher","first-page":"605","DOI":"10.3390\/diagnostics10080605","volume":"10","author":"E Kriegova","year":"2020","unstructured":"Kriegova E, Fillerova R, Kvapil P. Direct-RT-qPCR detection of SARS-CoV-2 without RNA extraction as part of a COVID-19 testing strategy: from sample to result in one hour. Diagnostics. 2020;10(8):605.","journal-title":"Diagnostics"},{"issue":"8","key":"9321_CR13","doi-asserted-by":"publisher","first-page":"2826","DOI":"10.3390\/ijms21082826","volume":"21","author":"R Lu","year":"2020","unstructured":"Lu R, Wu X, Wan Z, Li Y, Jin X, Zhang C. A novel reverse transcription loop-mediated isothermal amplification method for rapid detection of SARS-CoV-2. Int J Mol Sci. 2020;21(8):2826.","journal-title":"Int J Mol Sci"},{"issue":"15","key":"9321_CR14","doi-asserted-by":"publisher","first-page":"1492","DOI":"10.1056\/NEJMc2026172","volume":"383","author":"J Joung","year":"2020","unstructured":"Joung J, Ladha A, Saito M, Kim N-G, Woolley AE, Segel M, Barretto RPJ, Ranu A, Macrae RK, Faure G, Ioannidi EI, Krajeski RN, Bruneau R, Huang M-LW, Yu XG, Li JZ, Walker BD, Hung DT, Greninger AL, Jerome KR, Gootenberg JS, Abudayyeh OO, Zhang F. Detection of SARS-CoV-2 with SHERLOCK One-Pot testing. N Engl J Med. 2020;383(15):1492\u20134.","journal-title":"N Engl J Med"},{"issue":"1","key":"9321_CR15","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1016\/j.mcp.2003.09.001","volume":"18","author":"A Tichopad","year":"2004","unstructured":"Tichopad A, Didier A, Pfaffl MW. Inhibition of real-time RT\u2013PCR quantification due to tissue-specific contaminants. Mol Cell Probes. 2004;18(1):45\u201350.","journal-title":"Mol Cell Probes"},{"issue":"5","key":"9321_CR16","doi-asserted-by":"publisher","first-page":"1014","DOI":"10.1111\/j.1365-2672.2012.05384.x","volume":"113","author":"C Schrader","year":"2012","unstructured":"Schrader C, Schielke A, Ellerbroek L, Johne R. PCR inhibitors \u2013 occurrence, properties and removal. J Appl Microbiol. 2012;113(5):1014\u201326.","journal-title":"J Appl Microbiol"},{"issue":"20","key":"9321_CR17","doi-asserted-by":"publisher","first-page":"10247","DOI":"10.1021\/acs.analchem.5b01544","volume":"87","author":"MW Foster","year":"2015","unstructured":"Foster MW, Gerhardt G, Robitaille L, Plante P-L, Boivin G, Corbeil J, Moseley MA. Targeted proteomics of human metapneumovirus in clinical samples and viral cultures. Anal Chem. 2015;87(20):10247\u201354.","journal-title":"Anal Chem"},{"issue":"14","key":"9321_CR18","doi-asserted-by":"publisher","first-page":"5860","DOI":"10.1073\/pnas.0608638104","volume":"104","author":"A Wolf-Yadlin","year":"2007","unstructured":"Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci. 2007;104(14):5860\u20135.","journal-title":"Proc Natl Acad Sci"},{"issue":"73","key":"9321_CR19","doi-asserted-by":"publisher","first-page":"33762","DOI":"10.18632\/oncotarget.26031","volume":"9","author":"M Guerin","year":"2018","unstructured":"Guerin M, Gon\u00e7alves A, Toiron Y, Baudelet E, Pophillat M, Granjeaud S, Fourquet P, Jacot W, Tarpin C, Sabatier R, Agavnian E, Finetti P, Adelaide J, Birnbaum D, Ginestier C, Charafe-Jauffret E, Viens P, Bertucci F, Borg J-P, Camoin L. Development of parallel reaction monitoring (PRM)-based quantitative proteomics applied to HER2-Positive breast cancer. Oncotarget. 2018;9(73):33762\u201377.","journal-title":"Oncotarget"},{"issue":"13","key":"9321_CR20","doi-asserted-by":"publisher","first-page":"3556","DOI":"10.1021\/ac035229m","volume":"76","author":"KA Resing","year":"2004","unstructured":"Resing KA, Meyer-Arendt K, Mendoza AM, Aveline-Wolf LD, Jonscher KR, Pierce KG, Old WM, Cheung HT, Russell S, Wattawa JL, Goehle GR, Knight RD, Ahn NG. Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal Chem. 2004;76(13):3556\u201368.","journal-title":"Anal Chem"},{"issue":"S6","key":"9321_CR21","doi-asserted-by":"publisher","first-page":"S13","DOI":"10.1186\/1471-2105-9-S6-S13","volume":"9","author":"F-X Wu","year":"2008","unstructured":"Wu F-X, Gagn\u00e9 P, Droit A, Poirier GG. Quality assessment of peptide tandem mass spectra. BMC Bioinformat. 2008;9(S6):S13.","journal-title":"BMC Bioinformat"},{"issue":"14","key":"9321_CR22","doi-asserted-by":"publisher","first-page":"e2000107","DOI":"10.1002\/pmic.202000107","volume":"20","author":"D Gouveia","year":"2020","unstructured":"Gouveia D, Grenga L, Gaillard JC, Gallais F, Bellanger L, Pible O, Armengaud J. Shortlisting SARS-CoV-2 peptides for targeted studies from experimental data-dependent acquisition tandem mass spectrometry data. Proteomics. 2020;20(14):e2000107.","journal-title":"Proteomics"},{"issue":"1","key":"9321_CR23","doi-asserted-by":"publisher","first-page":"1712","DOI":"10.1080\/22221751.2020.1791737","volume":"9","author":"L Grenga","year":"2020","unstructured":"Grenga L, Gallais F, Pible O, et al. Shotgun proteomics analysis of SARS-CoV-2-infected cells and how it can optimize whole viral particle antigen production for vaccines. Emerging Microbes Infect. 2020;9(1):1712\u201321.","journal-title":"Emerging Microbes Infect"},{"issue":"68","key":"9321_CR24","first-page":"68","volume":"12","author":"AD Davidson","year":"2020","unstructured":"Davidson AD, Williamson MK, Lewis S, et al. Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein. Genome Biol. 2020;12(68):68.","journal-title":"Genome Biol"},{"issue":"1","key":"9321_CR25","doi-asserted-by":"publisher","first-page":"6201","DOI":"10.1038\/s41467-020-19925-0","volume":"11","author":"KHM Cardozo","year":"2020","unstructured":"Cardozo KHM, Lebkuchen A, Okai GG, Schuch RA, Viana LG, Olive AN, Lazari CDS, Fraga AM, Granato CFH, Pint\u00e3o MCT, Carvalho VM. Establishing a mass spectrometry-based system for rapid detection of SARS-CoV-2 in large clinical sample cohorts. Nat Commun. 2020;11(1):6201\u20136201.","journal-title":"Nat Commun"},{"issue":"11","key":"9321_CR26","doi-asserted-by":"publisher","first-page":"4389","DOI":"10.1021\/acs.jproteome.0c00280","volume":"19","author":"C Ihling","year":"2020","unstructured":"Ihling C, T\u00e4nzler D, Hagemann S, Kehlen A, H\u00fcttelmaier S, Arlt C, Sinz A. Mass spectrometric identification of SARS-CoV-2 proteins from gargle solution samples of COVID-19 patients. J Proteome Res. 2020;19(11):4389\u201392.","journal-title":"J Proteome Res"},{"key":"9321_CR27","doi-asserted-by":"publisher","first-page":"106121","DOI":"10.1016\/j.dib.2020.106121","volume":"32","author":"B Rivera","year":"2020","unstructured":"Rivera B, Leyva A, Portela MM, Moratorio G, Moreno P, Dur\u00e1n R, Limaa A. Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: Detection of viral proteins and host\u2019s biological processes altered by the infection. Data Brief. 2020;32:106121.","journal-title":"Data Brief"},{"key":"9321_CR28","doi-asserted-by":"publisher","DOI":"10.1111\/febs.15609","author":"HL Zeng","year":"2020","unstructured":"Zeng HL, Chen D, Yan J, Yang Q, Han QQ, Li SS, Cheng L. Proteomic characteristics of bronchoalveolar lavage fluid in critical COVID-19 patients. FEBS J. 2020;. https:\/\/doi.org\/10.1111\/febs.15609.","journal-title":"FEBS J"},{"issue":"1","key":"9321_CR29","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41392-020-00355-9","volume":"5","author":"L Leng","year":"2020","unstructured":"Leng L, Cao R, Ma J, Mou D, Zhu Y, Li W, Lv L, Gao D, Zhang S, Gong F, Zhao L, Qiu B, Xiang H, Hu Z, Feng Y, Dai Y, Zhao J, Wu Z, Li H, Zhong W. Pathological features of COVID-19-associated lung injury: a preliminary proteomics report based on clinical samples. Signal Transduct Targeted Therapy. 2020;5(1):1\u20139.","journal-title":"Signal Transduct Targeted Therapy"},{"issue":"3","key":"9321_CR30","doi-asserted-by":"publisher","first-page":"102135","DOI":"10.1016\/j.isci.2021.102135","volume":"24","author":"R Bankar","year":"2021","unstructured":"Bankar R, Suvarna K, Ghantasala S, Banerjee A, Biswas D, Choudhury M, Palanivel V, Salkar A, Verma A, Singh A, Mukherjee A, Pai MGJ, Roy J, Srivastava A, Badaya A, Agrawal S, Shrivastav O, Shastri J, Srivastava S. Proteomic investigation reveals dominant alterations of neutrophil degranulation and mRNA translation pathways in patients with COVID-19. iScience. 2021;24(3):102135.","journal-title":"iScience"},{"issue":"3","key":"9321_CR31","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1101\/gr.235028.118","volume":"29","author":"B Wen","year":"2019","unstructured":"Wen B, Wang X, Zhang B. PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations. Genome Res. 2019;29(3):485\u201393.","journal-title":"Genome Res"},{"issue":"4","key":"9321_CR32","doi-asserted-by":"publisher","first-page":"giaa025","DOI":"10.1093\/gigascience\/giaa025","volume":"9","author":"T McGowan","year":"2020","unstructured":"McGowan T, Johnson JE, Kumar P, Sajulga R, Mehta S, Jagtap PD, Griffin TJ. Multi-omics visualization platform: an extensible galaxy plug-in for multi-omics data visualization and exploration. GigaScience. 2020;9(4):giaa025.","journal-title":"GigaScience"},{"key":"9321_CR33","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformat. 2009;10:1\u20139.","journal-title":"BMC Bioinformat"},{"issue":"11","key":"9321_CR34","doi-asserted-by":"publisher","first-page":"4718","DOI":"10.1021\/acs.jproteome.0c00385","volume":"19","author":"JK Saunders","year":"2020","unstructured":"Saunders JK, Gaylord DA, Held NA, Symmonds N, Dupont CL, Shepherd A, Kinkade DB, Saito MA. METATRYP v 20: Metaproteomic least common ancestor analysis for taxonomic inference using specialized sequence assemblies\u2014standalone software and web servers for marine microorganisms and coronaviruses. J Proteome Res. 2020;19(11):4718\u201329.","journal-title":"J Proteome Res"},{"issue":"1","key":"9321_CR35","doi-asserted-by":"publisher","first-page":"6201","DOI":"10.1038\/s41467-020-19925-0","volume":"11","author":"KHM Cardozo","year":"2020","unstructured":"Cardozo KHM, Lebkuchen A, Okai GG, et al. Establishing a mass spectrometry-based system for rapid detection of SARS-CoV-2 in large clinical sample cohorts. Nat Commun. 2020;11(1):6201.","journal-title":"Nat Commun."},{"issue":"5","key":"9321_CR36","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1002\/pmic.201000595","volume":"11","author":"M Vaudel","year":"2011","unstructured":"Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L. SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics. 2011;11(5):996\u20139.","journal-title":"Proteomics"},{"issue":"1","key":"9321_CR37","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1038\/nbt.3109","volume":"33","author":"M Vaudel","year":"2015","unstructured":"Vaudel M, Burkhart JM, Zahedi RP, Oveland E, Berven FS, Sickmann A, Martens L, Barsnes H. PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nat Biotechnol. 2015;33(1):22\u20134.","journal-title":"Nat Biotechnol"},{"key":"9321_CR38","doi-asserted-by":"crossref","unstructured":"Orsburn BC, Jenkins C, Miller SM, Neely BA, Bumpus NN., In silico approach toward the identification of unique peptides from viral protein infection: Application to COVID-19. Cold Spring Harbor Laboratory; 2020. CR-MEDICINE-D-20-00111.","DOI":"10.1101\/2020.03.08.980383"},{"issue":"7","key":"9321_CR39","doi-asserted-by":"publisher","first-page":"1249","DOI":"10.1093\/bioinformatics\/bty770","volume":"35","author":"K Li","year":"2019","unstructured":"Li K, Vaudel M, Zhang B, Ren Y, Wen B. PDV: an integrative proteomics data viewer. Bioinformatics. 2019;35(7):1249\u201351.","journal-title":"Bioinformatics"},{"issue":"2","key":"9321_CR40","doi-asserted-by":"publisher","first-page":"606","DOI":"10.1021\/acs.jproteome.8b00716","volume":"18","author":"R Gurdeep Singh","year":"2019","unstructured":"Gurdeep Singh R, Tanca A, Palomba A, Van Der Jeugt F, Verschaffelt P, Uzzau S, Martens L, Dawyndt P, Mesuere B. Unipept 4.0: functional analysis of metaproteome data. J Proteome Res. 2019;18(2):606\u201315.","journal-title":"J Proteome Res"},{"issue":"7","key":"9321_CR41","doi-asserted-by":"publisher","first-page":"954","DOI":"10.1016\/j.cmi.2020.03.025","volume":"26","author":"MR Capobianchi","year":"2020","unstructured":"Capobianchi MR, Rueca M, Messina F, Giombini E, Carletti F, Colavita F, Castilletti C, Lalle E, Bordi L, Vairo F, Nicastri E, Ippolito G, Gruber CEM, Bartolini B. Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy. Clin Microbiol Infect. 2020;26(7):954\u20136.","journal-title":"Clin Microbiol Infect"},{"key":"9321_CR42","first-page":"ofaa403","volume-title":"In Virological characterization of the first 2 COVID-19 patients diagnosed in italy: phylogenetic analysis, virus shedding profile from different body sites, and antibody response kinetics","author":"F Colavita","year":"2020","unstructured":"Colavita F, Lapa D, Carletti F, Lalle E, Messina F, Rueca M, Matusali G, Meschi S, Bordi L, Marsella P. In Virological characterization of the first 2 COVID-19 patients diagnosed in italy: phylogenetic analysis, virus shedding profile from different body sites, and antibody response kinetics. Open Forum Infectious Diseases, Oxford: Oxford University Press US; 2020. p. ofaa403."},{"issue":"3","key":"9321_CR43","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1016\/j.cels.2016.02.001","volume":"2","author":"Y Pozniak","year":"2016","unstructured":"Pozniak Y, Balint-Lahat N, Rudolph JD, Lindskog C, Katzir R, Avivi C, Pont\u00e9n F, Ruppin E, Barshack I, Geiger T. System-wide clinical proteomics of breast cancer reveals global remodeling of tissue homeostasis. Cell Syst. 2016;2(3):172\u201384.","journal-title":"Cell Syst"},{"issue":"20","key":"9321_CR44","doi-asserted-by":"publisher","first-page":"6001","DOI":"10.1158\/0008-5472.CAN-18-1079","volume":"78","author":"G Yanovich","year":"2018","unstructured":"Yanovich G, Agmon H, Harel M, Sonnenblick A, Peretz T, Geiger T. Clinical proteomics of breast cancer reveals a novel layer of breast cancer classification. Can Res. 2018;78(20):6001\u201310.","journal-title":"Can Res"},{"issue":"1","key":"9321_CR45","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1186\/s12014-018-9219-8","volume":"15","author":"Y Chen","year":"2018","unstructured":"Chen Y, Huang A, Ao W, Wang Z, Yuan J, Song Q, Wei D, Ye H. Proteomic analysis of serum proteins from HIV\/AIDS patients with Talaromyces marneffei infection by TMT labeling-based quantitative proteomics. Clin Proteomics. 2018;15(1):40.","journal-title":"Clin Proteomics"},{"issue":"1","key":"9321_CR46","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.cels.2020.05.012","volume":"11","author":"CB Messner","year":"2020","unstructured":"Messner CB, Demichev V, Wendisch D, Michalick L, White M, Freiwald A, Textoris-Taube K, Vernardis SI, Egger A-S, Kreidl M. Ultra-high-throughput clinical proteomics reveals classifiers of COVID-19 infection. Cell Syst. 2020;11(1):11-24. e4.","journal-title":"Cell Syst"},{"issue":"50","key":"9321_CR47","doi-asserted-by":"publisher","first-page":"2000568","DOI":"10.2807\/1560-7917.ES.2020.25.50.2000568","volume":"25","author":"PS Wikramaratna","year":"2020","unstructured":"Wikramaratna PS, Paton RS, Ghafari M, Louren\u00e7o J. Estimating the false-negative test probability of SARS-CoV-2 by RT-PCR. Euro Surveill. 2020;25(50):2000568.","journal-title":"Euro Surveill"},{"issue":"9","key":"9321_CR48","doi-asserted-by":"publisher","first-page":"2383","DOI":"10.1074\/mcp.R113.027797","volume":"12","author":"D Shteynberg","year":"2013","unstructured":"Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW. Combining results of multiple search engines in proteomics. Mol Cell Proteom MCP. 2013;12(9):2383\u201393.","journal-title":"Mol Cell Proteom MCP"},{"issue":"6","key":"9321_CR49","doi-asserted-by":"publisher","first-page":"e04243","DOI":"10.1016\/j.heliyon.2020.e04243","volume":"6","author":"W-K Liu","year":"2020","unstructured":"Liu W-K, Xu D, Xu Y, Qiu S-Y, Zhang L, Wu H-K, Zhou R. Protein profile of well-differentiated versus un-differentiated human bronchial\/tracheal epithelial cells. Heliyon. 2020;6(6):e04243.","journal-title":"Heliyon"},{"key":"9321_CR50","first-page":"125","volume":"88","author":"C Marcus-Sekura","year":"1996","unstructured":"Marcus-Sekura C. Process changes and their effect on process evaluation for viral clearance. Dev Biol Stand. 1996;88:125\u201330.","journal-title":"Dev Biol Stand"},{"issue":"1","key":"9321_CR51","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1007\/s11373-005-9035-9","volume":"13","author":"C-K Chang","year":"2006","unstructured":"Chang C-K, Sue S-C, Yu T-H, Hsieh C-M, Tsai C-K, Chiang Y-C, Lee S-J, Hsiao H-H, Wu W-J, Chang W-L. Modular organization of SARS coronavirus nucleocapsid protein. J Biomed Sci. 2006;13(1):59\u201372.","journal-title":"J Biomed Sci"},{"key":"9321_CR52","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.antiviral.2013.12.009","volume":"103","author":"C-K Chang","year":"2014","unstructured":"Chang C-K, Hou M-H, Chang C-F, Hsiao C-D, Huang T-H. The SARS coronavirus nucleocapsid protein\u2013forms and functions. Antiviral Res. 2014;103:39\u201350.","journal-title":"Antiviral Res"},{"key":"9321_CR53","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1016\/S0065-3527(05)64006-7","volume":"64","author":"CA de Haan","year":"2005","unstructured":"de Haan CA, Rottier PJ. Molecular interactions in the assembly of coronaviruses. Adv Virus Res. 2005;64:165\u2013230.","journal-title":"Adv Virus Res"},{"issue":"1\u20132","key":"9321_CR54","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1016\/j.febslet.2004.09.009","volume":"576","author":"E Mortola","year":"2004","unstructured":"Mortola E, Roy P. Efficient assembly and release of SARS coronavirus-like particles by a heterologous expression system. FEBS Lett. 2004;576(1\u20132):174\u20138.","journal-title":"FEBS Lett"},{"key":"9321_CR55","doi-asserted-by":"publisher","first-page":"e57309","DOI":"10.7554\/eLife.57309","volume":"9","author":"YM Bar-On","year":"2020","unstructured":"Bar-On YM, Flamholz A, Phillips R, Milo R. Science Forum: SARS-CoV-2 (COVID-19) by the numbers. Elife. 2020;9:e57309.","journal-title":"Elife"},{"issue":"1","key":"9321_CR56","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1128\/JVI.75.1.506-512.2001","volume":"75","author":"JA Hiscox","year":"2001","unstructured":"Hiscox JA, Wurm T, Wilson L, Britton P, Cavanagh D, Brooks G. The coronavirus infectious bronchitis virus nucleoprotein localizes to the nucleolus. J Virol. 2001;75(1):506\u201312.","journal-title":"J Virol"},{"key":"9321_CR57","doi-asserted-by":"publisher","first-page":"112454","DOI":"10.1016\/j.bios.2020.112454","volume":"165","author":"N Ravi","year":"2020","unstructured":"Ravi N, Cortade DL, Ng E, Wang SX. Diagnostics for SARS-CoV-2 detection: A comprehensive review of the FDA-EUA COVID-19 testing landscape. Biosensors Bioelectron. 2020;165:112454.","journal-title":"Biosensors Bioelectron"},{"issue":"1","key":"9321_CR58","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1002\/0471142727.mb1025s88","volume":"90","author":"RL Gundry","year":"2010","unstructured":"Gundry RL, White MY, Murray CI, Kane LA, Fu Q, Stanley BA, Van Eyk JE. Preparation of proteins and peptides for mass spectrometry analysis in a bottom-up proteomics workflow. Curr Protocols Mol Biol. 2010;90(1):10\u201325.","journal-title":"Curr Protocols Mol Biol"},{"key":"9321_CR59","doi-asserted-by":"publisher","DOI":"10.1101\/2020.05.04.20091231","author":"J Joung","year":"2020","unstructured":"Joung J, Ladha A, Saito M, Segel M, Bruneau R, Huang M-LW, Kim N-G, Yu X, Li J, Walker BD, Greninger AL, Jerome KR, Gootenberg JS, Abudayyeh OO, Zhang F. Point-of-care testing for COVID-19 using SHERLOCK diagnostics. medRxiv. 2020. https:\/\/doi.org\/10.1101\/2020.05.04.20091231.","journal-title":"medRxiv"},{"issue":"3","key":"9321_CR60","first-page":"201","volume":"12","author":"M Dara","year":"2020","unstructured":"Dara M, Talebzadeh M. CRISPR\/Cas as a Potential Diagnosis Technique for COVID-19. Avicenna J Med Biotechnol. 2020;12(3):201\u20132.","journal-title":"Avicenna J Med Biotechnol"},{"key":"9321_CR61","unstructured":"Zhang F, Abudayyeh OO, Gootenberg JS. A protocol for detection of COVID-19 using CRISPR diagnostics. A protocol for detection of COVID-19 using CRISPR diagnostics. 2020, 8"},{"issue":"10","key":"9321_CR62","doi-asserted-by":"publisher","first-page":"3396","DOI":"10.1021\/acs.jproteome.8b00302","volume":"17","author":"DB Gutierrez","year":"2018","unstructured":"Gutierrez DB, Gant-Branum RL, Romer CE, Farrow MA, Allen JL, Dahal N, Nei Y-W, Codreanu SG, Jordan AT, Palmer LD. An integrated, high-throughput strategy for multiomic systems level analysis. J Proteome Res. 2018;17(10):3396\u2013408.","journal-title":"J Proteome Res"},{"issue":"5","key":"9321_CR63","doi-asserted-by":"publisher","first-page":"2337","DOI":"10.1021\/acs.jproteome.9b00023","volume":"18","author":"J Lee","year":"2019","unstructured":"Lee J, Kim H, Sohn A, Yeo I, Kim Y. Cost-effective automated preparation of serum samples for reproducible quantitative clinical proteomics. J Proteome Res. 2019;18(5):2337\u201345.","journal-title":"J Proteome Res"},{"issue":"1","key":"9321_CR64","doi-asserted-by":"publisher","first-page":"9111","DOI":"10.15252\/msb.20199111","volume":"16","author":"T M\u00fcller","year":"2020","unstructured":"M\u00fcller T, Kalxdorf M, Longuesp\u00e9e R, Kazdal DN, Stenzinger A, Krijgsveld J. Automated sample preparation with SP 3 for low-input clinical proteomics. Mol Syst Biol. 2020;16(1):9111.","journal-title":"Mol Syst Biol"},{"issue":"6","key":"9321_CR65","doi-asserted-by":"publisher","first-page":"giaa065","DOI":"10.1093\/gigascience\/giaa065","volume":"9","author":"H Rasche","year":"2020","unstructured":"Rasche H, Hiltemann S. Galactic Circos: User-friendly Circos plots within the Galaxy platform. Giga Science. 2020;9(6):giaa065.","journal-title":"Giga Science"}],"container-title":["Clinical Proteomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12014-021-09321-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12014-021-09321-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12014-021-09321-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,3]],"date-time":"2023-11-03T10:06:40Z","timestamp":1699006000000},"score":1,"resource":{"primary":{"URL":"https:\/\/clinicalproteomicsjournal.biomedcentral.com\/articles\/10.1186\/s12014-021-09321-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,10]]},"references-count":65,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["9321"],"URL":"https:\/\/doi.org\/10.1186\/s12014-021-09321-1","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.02.09.21251427","asserted-by":"object"}]},"ISSN":["1542-6416","1559-0275"],"issn-type":[{"value":"1542-6416","type":"print"},{"value":"1559-0275","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,5,10]]},"assertion":[{"value":"1 March 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 May 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 May 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"As this study utilized open-source mass spectrometry data of anonymous human subjects from previous studies, no ethics approval or consent to participate was needed.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"15"}}