Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34254058", "kind": "science-record", "revision": 6, "content_hash": "sha256:23a2347886daafe397e855e8324647d2f445ef629ce54d6733642765d21d5016", "created_at": "2026-11-01T15:41:43Z", "updated_at": "2026-11-01T21:25:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients.", "doi": "10.1021/jacsau.1c00048", "pmid": "34254058", "authors": ["Bart Van Puyvelde", "Katleen Van Uytfanghe", "Olivier Tytgat", "Laurence Van Oudenhove", "Ralf Gabriels", "Robbin Bouwmeester", "Simon Daled", "Tim Van Den Bossche", "Pathmanaban Ramasamy", "Sigrid Verhelst", "Laura De Clerck", "Laura Corveleyn", "Sander Willems", "Nathan Debunne", "Evelien Wynendaele", "Bart De Spiegeleer", "Peter Judak", "Kris Roels", "Laurie De Wilde", "Peter Van Eenoo", "Tim Reyns", "Marc Cherlet", "Emmie Dumont", "Griet Debyser", "Ruben t'Kindt", "Koen Sandra", "Surya Gupta", "Nicolas Drouin", "Amy Harms", "Thomas Hankemeier", "Donald J L Jones", "Pankaj Gupta", "Dan Lane", "Catherine S Lane", "Said El Ouadi", "Jean-Baptiste Vincendet", "Nick Morrice", "Stuart Oehrle", "Nikunj Tanna", "Steve Silvester", "Sally Hannam", "Florian C Sigloch", "Andrea Bhangu-Uhlmann", "Jan Claereboudt", "N Leigh Anderson", "Morteza Razavi", "Sven Degroeve", "Lize Cuypers", "Christophe Stove", "Katrien Lagrou", "Geert A Martens", "Dieter Deforce", "Lennart Martens", "Johannes P C Vissers", "Maarten Dhaenens"], "journal": "JACS Au", "year": 2021, "abstract": "Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, spread so rapidly across the globe. The policy response to such pandemics will always have to include accurate monitoring of the spread, as this provides one of the few alternatives to total lockdown. However, COVID-19 diagnosis is currently performed almost exclusively by reverse transcription polymerase chain reaction (RT-PCR). Although this is efficient, automatable, and acceptably cheap, reliance on one type of technology comes with serious caveats, as illustrated by recurring reagent and test shortages. We therefore developed an alternative diagnostic test that detects proteolytically digested SARS-CoV-2 proteins using mass spectrometry (MS). We established the Cov-MS consortium, consisting of 15 academic laboratories and several industrial partners to increase applicability, accessibility, sensitivity, and robustness of this kind of SARS-CoV-2 detection. This, in turn, gave rise to the Cov-MS Digital Incubator that allows other laboratories to join the effort, navigate, and share their optimizations and translate the assay into their clinic. As this test relies on viral proteins instead of RNA, it provides an orthogonal and complementary approach to RT-PCR using other reagents that are relatively inexpensive and widely available, as well as orthogonally skilled personnel and different instruments. Data are available via ProteomeXchange with identifier PXD022550.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry data generated during the current study are being shared through the Skyline Panorama Public interface for easy accessibility (https://panoramaweb.org/CovMS.url) and are being deposited to the ProteomeXchange Consortium via the PRIDE partner repository with data set identifier: PXD022550. The Supporting Information will be made available through the Microsoft Teams group: “Cov-MS Digital Incubator”. Please send an email to covms@ugent.be to obtain access.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34254058", "locator": "sections[25] \"Data Availability\" paragraph 2", "quote": "The mass spectrometry data generated during the current study are being shared through the Skyline Panorama Public interface for easy accessibility (https://panoramaweb.org/CovMS.url) and are being deposited to the ProteomeXchange Consortium via the PRIDE partner repository with data set identifier: PXD022550. The Supporting Information will be made available through the Microsoft Teams group: “Cov-MS Digital Incubator”. Please send an email to covms@ugent.be to obtain access."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:34254058"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD022550"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD022550"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34254058", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1021/jacsau.1c00048", "sha256": "sha256:f50ccfc7dbffb0ffedd165cda625fb77bc0823b7c523554829ee9d6d215293b3", "bytes": 68449, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1021/jacsau.1c00048", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8230961", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD022550", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD022550", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD022550", "version": null, "note": "The mass spectrometry data generated during the current study are being shared through the Skyline Panorama Public interface for easy accessibility (https://panoramaweb.org/CovMS.url) and are being deposited to the ProteomeXchange Consortium via the PRIDE partner repository with data set identifier: PXD022550. The Supporting Information will be made available through the Microsoft Teams group: “Cov-MS Digital Incubator”. Please send an email to covms@ugent.be to obtain access.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry data generated during the current study are being shared through the Skyline Panorama Public interface for easy accessibility (https://panoramaweb.org/CovMS.url) and are being deposited to the ProteomeXchange Consortium via the PRIDE partner repository with data set identifier: PXD022550. The Supporting Information will be made available through the Microsoft Teams group: “Cov-MS Digital Incubator”. Please send an email to covms@ugent.be to obtain access.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Cov-MS: a community-based template assay for clinical MS-based protein detection in Sars-Cov-2 patients", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD022550 not downloaded", "asset:data:geo:PXD022550 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "regression_modelling", "specific": "ols", "label": "Regression modelling", "dsl_operations": ["ols_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.8, "band": "high", "quote": "linear regression"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["ols_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ols."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD022550"], "resolved_accessions": ["PXD022550"], "statements": ["The mass spectrometry data generated during the current study are being shared through the Skyline Panorama Public interface for easy accessibility (https://panoramaweb.org/CovMS.url) and are being deposited to the ProteomeXchange Consortium via the PRIDE partner repository with data set identifier: PXD022550. The Supporting Information will be made available through the Microsoft Teams group: “Cov-MS Digital Incubator”. Please send an email to covms@ugent.be to obtain access."], "basis": "The paper names PXD022550 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["ols_fit"], "assets": ["source:pmid:34254058", "data:geo:PXD022550"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD022550"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:41:08Z", "independence": "single_reader"}, "evidence_check": {"method": "absent", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 45908, "completion_tokens": 2428, "cached_tokens": 15368}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:34254058", "type": "paper", "label": "pmid:34254058"}, {"id": "source:pmid:34254058", "type": "manuscript", "label": "PMID 34254058 full text"}, {"id": "data:geo:PXD022550", "type": "dataset", "label": "GEO PXD022550"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34254058", "type": "paper", "label": "pmid:34254058"}, {"id": "source:pmid:34254058", "type": "manuscript", "label": "PMID 34254058 full text"}, {"id": "data:geo:PXD022550", "type": "dataset", "label": "GEO PXD022550"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34254058", "type": "extraction", "used": ["source:pmid:34254058"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD022550", "type": "accession_resolution", "used": ["data:geo:PXD022550"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:34254058", "parent_hash": "sha256:8882cae425dad03d9b1357fc89e1402df00749811333e65c218f3bdd04baf695", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD022550 licence not read", "asset:data:geo:PXD022550 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["lytically digested SARS-CoV-2 proteins using mass spectrometry (MS). We established the Cov-MS consortium,", "rotein for retention time standardization in proteomics studies) retention time standard peptides we"], "order_basis": "paper_text_order:832", "id": "assay:1"}, {"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["ols_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["linear regression"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}