A Carrier-Based Quantitative Proteomics Method Applied to Biomarker Discovery in Pericardial Fluid.

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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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