Comprehensive Library Generation for Identification and Quantification of Endometrial Cancer Protein Biomarkers in Cervico-Vaginal Fluid.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34359700", "kind": "science-record", "revision": 6, "content_hash": "sha256:c8f0d4f8bef5eb22442da58567dac6815911403daebd1d7ecc432a444a05a817", "created_at": "2026-11-01T15:41:47Z", "updated_at": "2026-11-01T21:25:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive Library Generation for Identification and Quantification of Endometrial Cancer Protein Biomarkers in Cervico-Vaginal Fluid.", "doi": "10.3390/cancers13153804", "pmid": "34359700", "authors": ["Kelechi Njoku", "Davide Chiasserini", "Bethany Geary", "Andrew Pierce", "Eleanor R Jones", "Anthony D Whetton", "Emma J Crosbie"], "journal": "Cancers", "year": 2021, "abstract": "Endometrial cancer is the most common gynaecological malignancy in high-income countries and its incidence is rising. Early detection, aided by highly sensitive and specific biomarkers, has the potential to improve outcomes as treatment can be provided when it is most likely to effect a cure. Sequential window acquisition of all theoretical mass spectra (SWATH-MS), an accurate and reproducible platform for analysing biological samples, offers a technological advance for biomarker discovery due to its reproducibility, sensitivity and potential for data re-interrogation. SWATH-MS requires a spectral library in order to identify and quantify peptides from multiplexed mass spectrometry data. Here we present a bespoke spectral library of 154,206 transitions identifying 19,394 peptides and 2425 proteins in the cervico-vaginal fluid of postmenopausal women with, or at risk of, endometrial cancer. We have combined these data with a library of over 6000 proteins generated based on mass spectrometric analysis of two endometrial cancer cell lines. This unique resource enables the study of protein biomarkers for endometrial cancer detection in cervico-vaginal fluid. Data are available via ProteomeXchange with unique identifier PXD025925.", "claims": [{"id": "claim-method", "statement": "Principal component analysis (PCA) and t-distributed stochastic neighbour embedding (t-SNE) plots were then used to assess degree of separation between groups and shown in Figure 10.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34359700", "locator": "sections[19] \"3.3.2. Real World Application of Spectral Library for Biomarker Discovery\" paragraph 4", "quote": "Principal component analysis (PCA) and t-distributed stochastic neighbour embedding (t-SNE) plots were then used to assess degree of separation between groups and shown in Figure 10."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All datasets have been deposited in ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org/ (accessed on 26 July 2021)) via the PRIDE partner repository with the dataset identifier PXD025925.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34359700", "locator": "sections[27] \"Data Availability Statement\" paragraph 2", "quote": "All datasets have been deposited in ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org/ (accessed on 26 July 2021)) via the PRIDE partner repository with the dataset identifier PXD025925."}], "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:34359700"], "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:PXD025925"], "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:PXD025925"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34359700", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/cancers13153804", "sha256": "sha256:66704eb3872711fce12f7b3d02cb63235907115631e3d44e830e407a9456d5c0", "bytes": 66738, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/cancers13153804", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8345211", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD025925", "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=PXD025925", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD025925", "version": null, "note": "All datasets have been deposited in ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org/ (accessed on 26 July 2021)) via the PRIDE partner repository with the dataset identifier PXD025925.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All datasets have been deposited in ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org/ (accessed on 26 July 2021)) via the PRIDE partner repository with the dataset identifier PXD025925.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Comprehensive spectral  library generation for identification and quantification of endometrial cancer protein biomarkers in cervico-vaginal fluid", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34359700:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d7874e02bb135d41244056e0cc2d9717a86d1dbf9e091cfbcaaad5cc1db08ccf", "bytes": 813, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#cancers-13-03804-t001", "version": null, "note": "Eligibility criteria for case and control selection.", "structure": {"pmcid": "PMC8345211", "section_index": 3, "section_title": "2.1. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD025925"], "resolved_accessions": ["PXD025925"], "statements": ["All datasets have been deposited in ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org/ (accessed on 26 July 2021)) via the PRIDE partner repository with the dataset identifier PXD025925."], "basis": "The paper names PXD025925 in ProteomeXchange Consortium and the accession resolves in the repository. 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Cell lines were cultured in DMEM growth medium (Gibco Life Technologi", "r Mycoplasma prior to usage. Cell lines were cultured in DMEM growth medium (Gibco Life Technologies;"], "order_basis": "paper_text_order:2518", "id": "assay:1"}, {"role": "analysis", "definition_id": "principal_component_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pca_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Principal component analysis (PCA) and t-distributed stochastic neighbour embedding (t-SNE) plots were then used to assess degree of separation between groups and shown in Figure 10."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}