{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39004188", "kind": "science-record", "revision": 3, "content_hash": "sha256:195e1b0e273810a3aa87c99211c77ef651b05f033303962e1bab9bddfe854dd3", "created_at": "2026-11-01T20:29:04Z", "updated_at": "2026-11-01T22:12:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Carrier-Based Quantitative Proteomics Method Applied to Biomarker Discovery in Pericardial Fluid.", "doi": "10.1016/j.mcpro.2024.100812", "pmid": "39004188", "authors": ["Amanda J Campbell", "Samir Cakar", "Nicolai B Palstrøm", "Lars P Riber", "Lars M Rasmussen", "Hans C Beck"], "journal": "Molecular & cellular proteomics : MCP", "year": 2024, "abstract": "Data-dependent liquid chromatography tandem mass spectrometry is challenged by the large concentration range of proteins in plasma and related fluids. We adapted the SCoPE method from single-cell proteomics to pericardial fluid, where a myocardial tissue carrier was used to aid protein quantification. The carrier proteome and patient samples were labeled with distinct isobaric labels, which allowed separate quantification. Undepleted pericardial fluid from patients with type 2 diabetes mellitus and/or heart failure undergoing heart surgery was analyzed with either a traditional liquid chromatography tandem mass spectrometry method or with the carrier proteome. In total, 1398 proteins were quantified with a carrier, compared to 265 without, and a higher proportion of these proteins were of myocardial origin. The number of differentially expressed proteins also increased nearly four-fold. For patients with both heart failure and type 2 diabetes mellitus, pathway analysis of upregulated proteins demonstrated the enrichment of immune activation, blood coagulation, and stress pathways. Overall, our work demonstrates the applicability of a carrier for enhanced protein quantification in challenging biological matrices such as pericardial fluid, with potential applications for biomarker discovery. Mass spectrometry data are available via ProteomeXchange with identifier PXD053450.", "claims": [{"id": "claim-method", "statement": "hereafter p-values were calculated using a two-sided Student's t test assuming equal variance comparing each experimental group to the control group.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39004188", "locator": "sections[6] \"Experimental Design and Statistical Rationale\" paragraph 2", "quote": "hereafter p-values were calculated using a two-sided Student's t test assuming equal variance comparing each experimental group to the control group."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Mass spectrometry data (.raw) and database search files (.mztab and .pdResult) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (36) with the dataset identifier PXD053450.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39004188", "locator": "sections[28] \"Data availability\" paragraph 2", "quote": "Mass spectrometry data (.raw) and database search files (.mztab and .pdResult) have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (36) with the dataset identifier PXD053450."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Adding a myocardial carrier increased quantified proteins from 265 to 1398 and increased the number of differentially expressed proteins from 41 to 156.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39004188", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In total, 1398 proteins were quantified with a carrier, compared to 265 without, and a higher proportion of these proteins were of myocardial origin."}, {"asset": "source:pmid:39004188", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The number of differentially expressed proteins also increased nearly four-fold."}, {"asset": "source:pmid:39004188", "locator": "sections[24] \"Patient Experiment: The Carrier Proteome Increased the Number of Differentially Expressed Proteins\" paragraph 2", "quote": "When the carrier proteome was added to samples, 156 proteins were differentially expressed in pericardial fluid among the three experimental groups (Supplemental Table S3). For comparison, when pericardial fluid samples were run with no carrier proteome, 41 proteins were differentially expressed among the three experimental groups (Supplemental Table S4)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Adding a myocardial carrier increased quantified proteins from 265 to 1398 and increased the number of differentially expressed proteins from 41 to 156.", "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:39004188"], "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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At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. 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The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. 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The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. 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