Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: Detection of viral proteins and host's biological processes altered by the infection.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32835036", "kind": "science-record", "revision": 7, "content_hash": "sha256:6ed7741cdb8fdcc455dea102fd4f57cf2d693a59c5bce9ab91f170ca16320c63", "created_at": "2026-11-01T15:41:08Z", "updated_at": "2026-11-01T22:02:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: Detection of viral proteins and host's biological processes altered by the infection.", "doi": "10.1016/j.dib.2020.106121", "pmid": "32835036", "authors": ["Bernardina Rivera", "Alejandro Leyva", "María Magdalena Portela", "Gonzalo Moratorio", "Pilar Moreno", "Rosario Durán", "Analía Lima"], "journal": "Data in brief", "year": 2020, "abstract": "Since January 2020, the world is facing the COVID-19 pandemic caused by SARS-CoV-2. In a big effort to cope with this outbreak, two Uruguayan institutions, Institut Pasteur de Montevideo and Universidad de la República, have developed and implemented a diagnosis pipeline based on qRT-PCR using entirely local resources. In this context, we performed comparative quantitative proteomic analysis from oro- and naso-pharyngeal swabs used for diagnosis. Tryptic peptides obtained from five positive and five negative samples were analysed by nano-LC-MS/MS using a Q-Exactive Plus mass spectrometer. Data analysis was performed using PatternLab for Proteomics software. From all SARS-CoV-2 positive swabs we were able to detect peptides of the SARS-CoV-2 nucleoprotein that encapsulates and protect the RNA genome. Additionally, we detected an average of 1100 human proteins from each sample. The most abundant proteins exclusively detected in positive swabs were \"Guanylate-binding protein 1\", \"Tapasin\" and \"HLA class II histocompatibility antigen DR beta chain\". The biological processes overrepresented in infected host cells were \"SRP-dependent cotranslational protein targeting to membrane\", \"nuclear-transcribed mRNA catabolic process, nonsense-mediated decay\", \"viral transcription\" and \"translational initiation\". Data is available via ProteomeXchange with identifier PXD020394. We expect that this data can contribute to the future development of mass spectrometry based approaches for COVID-19 diagnosis. Also, we share this preliminary proteomic characterization concerning the host response to infection for its reuse in basic investigation.", "claims": [{"id": "claim-method", "statement": "Fisher exact was used as statistical analysis with Bonferroni correction for multiple testing.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32835036", "locator": "sections[3] \"Data description\" paragraph 5", "quote": "Fisher exact was used as statistical analysis with Bonferroni correction for multiple testing."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All proteomic data have been deposited into the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD020394 and is available [5].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32835036", "locator": "sections[10] \"Mass spectrometry data repository\" paragraph 2", "quote": "All proteomic data have been deposited into the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD020394 and is available [5]."}], "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:32835036"], "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. 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