Label-free LC-MSe in tissue and serum reveals protein networks underlying differences between benign and malignant serous ovarian tumors.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25265318", "kind": "science-record", "revision": 6, "content_hash": "sha256:7cf4d43ea650f8d7ae3890f10790ab7d2546fab1a38b18ea87e9ccc9a5876af2", "created_at": "2026-11-01T15:40:06Z", "updated_at": "2026-11-01T21:19:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Label-free LC-MSe in tissue and serum reveals protein networks underlying differences between benign and malignant serous ovarian tumors.", "doi": "10.1371/journal.pone.0108046", "pmid": "25265318", "authors": ["Wouter Wegdam", "Carmen A Argmann", "Gertjan Kramer", "Johannes P Vissers", "Marrije R Buist", "Gemma G Kenter", "Johannes M F G Aerts", "Danielle Meijer", "Perry D Moerland"], "journal": "PloS one", "year": 2014, "abstract": "PURPOSE: To identify proteins and (molecular/biological) pathways associated with differences between benign and malignant epithelial ovarian tumors.\nEXPERIMENTAL PROCEDURES: Serum of six patients with a serous adenocarcinoma of the ovary was collected before treatment, with a control group consisting of six matched patients with a serous cystadenoma. In addition to the serum, homogeneous regions of cells exhibiting uniform histology were isolated from benign and cancerous tissue by laser microdissection. We subsequently employed label-free liquid chromatography tandem mass spectrometry (LC-MSe) to identify proteins in these serum and tissues samples. Analyses of differential expression between samples were performed using Bioconductor packages and in-house scripts in the statistical software package R. Hierarchical clustering and pathway enrichment analyses were performed, as well as network enrichment and interactome analysis using MetaCore.\nRESULTS: In total, we identified 20 and 71 proteins that were significantly differentially expressed between benign and malignant serum and tissue samples, respectively. The differentially expressed protein sets in serum and tissue largely differed with only 2 proteins in common. MetaCore network analysis, however inferred GCR-alpha and Sp1 as common transcriptional regulators. Interactome analysis highlighted 14-3-3 zeta/delta, 14-3-3 beta/alpha, Alpha-actinin 4, HSP60, and PCBP1 as critical proteins in the tumor proteome signature based on their relative overconnectivity. The data have been deposited to the ProteomeXchange with identifier PXD001084.\nDISCUSSION: Our analysis identified proteins with both novel and previously known associations to ovarian cancer biology. Despite the small overlap between differentially expressed protein sets in serum and tissue, APOA1 and Serotransferrin were significantly lower expressed in both serum and cancer tissue samples, suggesting a tissue-derived effect in serum. Pathway and subsequent interactome analysis also highlighted common regulators in serum and tissue samples, suggesting a yet unknown role for PCBP1 in ovarian cancer pathophysiology.", "claims": [{"id": "claim-method", "statement": "Differentially expressed proteins between benign and malignant tumors were detected using a moderated t-test. The mass spectrometry proteomics data have been deposited to the ProteomeXchange consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001084.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25265318", "locator": "sections[8] \"Statistical analyses\" paragraph 3", "quote": "Differentially expressed proteins between benign and malignant tumors were detected using a moderated t-test."}, {"asset": "source:pmid:25265318", "locator": "sections[18] \"Data Availability\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001084."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The authors confirm that all data underlying the findings are fully available without restriction. The mass spectrometry proteomics data have been deposited to the ProteomeXchange consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001084.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25265318", "locator": "sections[18] \"Data Availability\" paragraph 2", "quote": "The authors confirm that all data underlying the findings are fully available without restriction. The mass spectrometry proteomics data have been deposited to the ProteomeXchange consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001084."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 20 significantly differentially expressed serum proteins and 71 significantly differentially expressed tissue proteins between benign and malignant ovarian tumors, with only two proteins shared between the two signatures.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25265318", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In total, we identified 20 and 71 proteins that were significantly differentially expressed between benign and malignant serum and tissue samples, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 20 significantly differentially expressed serum proteins and 71 significantly differentially expressed tissue proteins between benign and malignant ovarian tumors, with only two proteins shared between the two signatures.", "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:25265318"], "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:GSE12172"], "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:GSE12172"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:25265318", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0108046", "sha256": "sha256:90d462f33c7dec2ece50a6f7cbf6136cc669587bc5f6e0a7351c1de79ba8ccb3", "bytes": 58108, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0108046", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4180266", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12172", "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=GSE12172", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12172", "version": null, "note": "The authors confirm that all data underlying the findings are fully available without restriction. 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