{"doi":"10.1016/j.ebiom.2021.103465","title":"A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens","abstract":"BACKGROUND: The COVID-19 pandemic caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has overwhelmed health systems worldwide and highlighted limitations of diagnostic testing. Several types of diagnostic tests including RT-PCR-based assays and antigen detection by lateral flow assays, each with their own strengths and weaknesses, have been developed and deployed in a short time. METHODS: Here, we describe an immunoaffinity purification approach followed a by high resolution mass spectrometry-based targeted qualitative assay capable of detecting SARS-CoV-2 viral antigen from nasopharyngeal swab samples. Based on our discovery experiments using purified virus, recombinant viral protein and nasopharyngeal swab samples from COVID-19 positive patients, nucleocapsid protein was selected as a target antigen. We then developed an automated antibody capture-based workflow coupled to targeted high-field asymmetric waveform ion mobility spectrometry (FAIMS) - parallel reaction monitoring (PRM) assay on an Orbitrap Exploris 480 mass spectrometer. An ensemble machine learning-based model for determining COVID-19 positive samples was developed using fragment ion intensities from the PRM data. FINDINGS: The optimized targeted assay, which was used to analyze 88 positive and 88 negative nasopharyngeal swab samples for validation, resulted in 98% (95% CI = 0.922-0.997) (86/88) sensitivity and 100% (95% CI = 0.958-1.000) (88/88) specificity using RT-PCR-based molecular testing as the reference method. INTERPRETATION: Our results demonstrate that direct detection of infectious agents from clinical samples by tandem mass spectrometry-based assays have potential to be deployed as diagnostic assays in clinical laboratories, which has hitherto been limited to analysis of pure microbial cultures. FUNDING: This study was supported by DBT/Wellcome Trust India Alliance Margdarshi Fellowship grant IA/M/15/1/502023 awarded to AP and the generosity of Eric and Wendy Schmidt.","journal":"EBioMedicine","year":2021,"id":153071,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":71,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9527,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":235323,"name":"Patrick M. Vanderboom","orcid":"0000-0003-1341-1733","position":1,"is_corresponding":false},{"id":554728,"name":"Anthony Maus","orcid":"0000-0003-3006-6265","position":2,"is_corresponding":false},{"id":555354,"name":"Jennifer Kemp","orcid":null,"position":3,"is_corresponding":false},{"id":555355,"name":"Kari M. Gurtner","orcid":null,"position":4,"is_corresponding":false},{"id":371635,"name":"Anil K. Madugundu","orcid":"0000-0003-4274-7316","position":5,"is_corresponding":false},{"id":554729,"name":"Sandip Chavan","orcid":"0000-0002-8469-7882","position":6,"is_corresponding":false},{"id":54150,"name":"Jane A. Peterson","orcid":null,"position":7,"is_corresponding":false},{"id":298642,"name":"Benjamin J. Madden","orcid":"0000-0001-9167-8535","position":8,"is_corresponding":false},{"id":554730,"name":"Kiran K. Mangalaparthi","orcid":"0000-0002-5791-727X","position":9,"is_corresponding":false},{"id":554731,"name":"Dong‐Gi Mun","orcid":"0000-0003-3588-3440","position":10,"is_corresponding":false},{"id":554732,"name":"Smrita Singh","orcid":"0000-0002-0394-3069","position":11,"is_corresponding":false},{"id":554733,"name":"Benjamin R. Kipp","orcid":"0000-0001-9477-0118","position":12,"is_corresponding":false},{"id":235319,"name":"Surendra Dasari","orcid":"0000-0002-7972-3556","position":13,"is_corresponding":false},{"id":397360,"name":"Ravinder J. Singh","orcid":"0000-0003-4538-6544","position":14,"is_corresponding":false},{"id":554734,"name":"Stefan K. Grebe","orcid":"0000-0003-1736-3206","position":15,"is_corresponding":false},{"id":60408,"name":"Akhilesh Pandey","orcid":"0000-0001-9943-6127","position":16,"is_corresponding":false},{"id":371634,"name":"Santosh Renuse","orcid":"0000-0002-4051-5637","position":0,"is_corresponding":true}],"reference_count":45,"raw_metadata":null,"created_at":"2026-07-18T23:43:39.820288Z","pmid":"34229274","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}