Quantitative site- and structure-specific N-glycoproteomics characterization of differential N-glycosylation in MCF-7/ADR cancer stem cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32042278", "kind": "science-record", "revision": 6, "content_hash": "sha256:a304cffb51150cdd6f82d54c16baafced131bb1e7adbf246c303682bd2a5dadd", "created_at": "2026-11-01T15:40:56Z", "updated_at": "2026-11-01T21:22:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Quantitative site- and structure-specific N-glycoproteomics characterization of differential N-glycosylation in MCF-7/ADR cancer stem cells.", "doi": "10.1186/s12014-020-9268-7", "pmid": "32042278", "authors": ["Feifei Xu", "Yue Wang", "Kaijie Xiao", "Yechen Hu", "Zhixin Tian", "Yun Chen"], "journal": "Clinical proteomics", "year": 2020, "abstract": "BACKGROUND: Cancer stem cells (CSCs) are reported to be responsible for tumor initiation, progression, metastasis, and therapy resistance where P-glycoprotein (P-gp) as well as other glycoproteins are involved. Identification of these glycoprotein markers is critical for understanding the resistance mechanism and developing therapeutics.\nMETHODS: In this study, we report our comparative and quantitative site- and structure-specific N-glycoproteomics study of MCF-7/ADR cancer stem cells (CSCs) vs. MCF-7/ADR cells. With zic-HILIC enrichment, isotopic diethyl labeling, RPLC-MS/MS (HCD) analysis and GPSeeker DB search, differentially expressed N-glycosylation was quantitatively characterized at the intact N-glycopeptide level.\nRESULTS: 4016 intact N-glycopeptides were identified with spectrum-level FDR ≤ 1%. With the criteria of ≥ 1.5 fold change and p value < 0.05, 247 intact N-glycopeptides were found differentially expressed in MCF-7/ADR CSCs as putative markers. Raw data are available via ProteomeXchange with identifier PXD013836.\nCONCLUSIONS: Quantitative site- and structure-specific N-glycoproteomics characterization may help illustrate the cell stemness property.", "claims": [{"id": "claim-method", "statement": "For the intact N-glycopeptides quantitated at least twice, the p value was calculated using t-test [19]; and the intact N-glycopeptides with a fold change of no less than 1.5 and p value no bigger than 0.05 were classified as differentially expressed intact N-glycopeptides.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32042278", "locator": "sections[10] \"Relative quantitation of differentially expressed intact N-glycopeptides in MCF-7/ADR CSCs relative to MCF-7/ADR using the quantitation module GPSeekerQuan in GPSeeker\" paragraph 2", "quote": "For the intact N-glycopeptides quantitated at least twice, the p value was calculated using t-test [19]; and the intact N-glycopeptides with a fold change of no less than 1.5 and p value no bigger than 0.05 were classified as differentially expressed intact N-glycopeptides."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The three RPLC-MS/MS (HCD) technical replicate datasets (.raw) are freely available at ProteomeXchange Consortium via the PRIDE partner repository [27]: PXD013836.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32042278", "locator": "sections[23] \"Availability of data and materials\" paragraph 2", "quote": "The three RPLC-MS/MS (HCD) technical replicate datasets (.raw) are freely available at ProteomeXchange Consortium via the PRIDE partner repository [27]: PXD013836."}], "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:32042278"], "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:PXD013836"], "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:PXD013836"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32042278", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12014-020-9268-7", "sha256": "sha256:e6e3fa7a308f36009fac815a3853dadb33c0972b3e15eefad9f86dd798797460", "bytes": 42913, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12014-020-9268-7", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7001331", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD013836", "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=PXD013836", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD013836", "version": null, "note": "The three RPLC-MS/MS (HCD) technical replicate datasets (.raw) are freely available at ProteomeXchange Consortium via the PRIDE partner repository [27]: PXD013836.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The three RPLC-MS/MS (HCD) technical replicate datasets (.raw) are freely available at ProteomeXchange Consortium via the PRIDE partner repository [27]: PXD013836.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Human Breast LC-MSMS -  Quantitative site- and structure-specific N-glycoproteomics characterization of differential N-glycosylation in MCF-7/ADR cancer stem cells", "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:PXD013836 not downloaded", "asset:data:geo:PXD013836 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For the intact N-glycopeptides quantitated at least twice, the p value was calculated using t-test [19]; and the intact N-glycopeptides with a fold change of no less than 1.5 and p value no bigger than 0.05 were classified as differentially expressed intact N-glycopeptides."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (t-test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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