Characterizing age-related changes in intact mitochondrial proteoforms in murine hearts using quantitative top-down proteomics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39343872", "kind": "science-record", "revision": 2, "content_hash": "sha256:2373abbb7558cc8092ec40c39fc3bf581a5eb8bad8332dde01ae1dbd359f7f3a", "created_at": "2026-11-01T20:29:32Z", "updated_at": "2026-11-01T21:34:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Characterizing age-related changes in intact mitochondrial proteoforms in murine hearts using quantitative top-down proteomics.", "doi": "10.1186/s12014-024-09509-1", "pmid": "39343872", "authors": ["Andrea Ramirez-Sagredo", "Anju Teresa Sunny", "Kellye A Cupp-Sutton", "Trishika Chowdhury", "Zhitao Zhao", "Si Wu", "Ying Ann Chiao"], "journal": "Clinical proteomics", "year": 2024, "abstract": "BACKGROUND: Cardiovascular diseases (CVDs) are the leading cause of death worldwide, and the prevalence of CVDs increases markedly with age. Due to the high energetic demand, the heart is highly sensitive to mitochondrial dysfunction. The complexity of the cardiac mitochondrial proteome hinders the development of effective strategies that target mitochondrial dysfunction in CVDs. Mammalian mitochondria are composed of over 1000 proteins, most of which can undergo post-translational modifications (PTMs). Top-down proteomics is a powerful technique for characterizing and quantifying proteoform sequence variations and PTMs. However, there are still knowledge gaps in the study of age-related mitochondrial proteoform changes using this technique. In this study, we used top-down proteomics to identify intact mitochondrial proteoforms in young and old hearts and determined changes in protein abundance and PTMs in cardiac aging.\nMETHODS: Intact mitochondria were isolated from the hearts of young (4-month-old) and old (24-25-month-old) mice. The mitochondria were lysed, and mitochondrial lysates were subjected to denaturation, reduction, and alkylation. For quantitative top-down analysis, there were 12 runs in total arising from 3 biological replicates in two conditions, with technical duplicates for each sample. The collected top-down datasets were deconvoluted and quantified, and then the proteoforms were identified.\nRESULTS: From a total of 12 LC-MS/MS runs, we identified 134 unique mitochondrial proteins in the different sub-mitochondrial compartments (OMM, IMS, IMM, matrix). 823 unique proteoforms in different mass ranges were identified. Compared to cardiac mitochondria of young mice, 7 proteoforms exhibited increased abundance and 13 proteoforms exhibited decreased abundance in cardiac mitochondria of old mice. Our analysis also detected PTMs of mitochondrial proteoforms, including N-terminal acetylation, lysine succinylation, lysine acetylation, oxidation, and phosphorylation. Data are available via ProteomeXchange with the identifier PXD051505.\nCONCLUSION: By combining mitochondrial protein enrichment using mitochondrial fractionation with quantitative top-down analysis using ultrahigh-pressure liquid chromatography (UPLC)-MS and label-free quantitation, we successfully identified and quantified intact proteoforms in the complex mitochondrial proteome. Using this approach, we detected age-related changes in abundance and PTMs of mitochondrial proteoforms in the heart.", "claims": [{"id": "claim-method", "statement": "Student’s t-tests were used to determine the statistical significance of the fold change of each proteoform between the young and old hearts [39].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39343872", "locator": "sections[3] \"Results\" paragraph 7", "quote": "Student’s t-tests were used to determine the statistical significance of the fold change of each proteoform between the young and old hearts [39]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "No datasets were generated or analysed during the current study.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39343872", "locator": "sections[9] \"Data availability\" paragraph 2", "quote": "No datasets were generated or analysed during the current study."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Twenty mitochondrial proteoforms were differentially expressed between young and old mouse hearts: 13 decreased and 7 increased in abundance in old mice.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39343872", "locator": "sections[3] \"Results\" paragraph 8", "quote": "Overall, 20 proteoforms were differentially expressed between the young and old hearts."}, {"asset": "source:pmid:39343872", "locator": "sections[3] \"Results\" paragraph 8", "quote": "Thirteen (13) proteoforms were decreased in abundance and 7 proteoforms were increased in abundance in the old mice (Supplementary Table 2)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Twenty mitochondrial proteoforms were differentially expressed between young and old mouse hearts: 13 decreased and 7 increased in abundance in old mice.", "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:39343872"], "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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Animals. Male C57Bl6 mice were group-housed and maintained on a 14-h light/", "e used for the study. For sample collection, mice were anesthetized with isoflurane and the hearts"], "order_basis": "paper_text_order:27", "id": "assay:1"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["in murine hearts using quantitative top-down proteomics.", "translational modifications (PTMs). Top-down proteomics is a powerful technique for characterizing a", "ith manual evaluation. The mass spectrometry proteomics data have been deposited to the ProteomeXcha", "were identified. RESULTS: From a total of 12 LC-MS/MS runs, we identified 134 unique mitochondrial"], "order_basis": "paper_text_order:71", "id": "assay:2"}]}