Identification of cardiac myofilament protein isoforms using multiple mass spectrometry based approaches.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:24974818", "kind": "science-record", "revision": 5, "content_hash": "sha256:683e90641f0ca9e31edb952e97116b672b23daf2abfd25802c4dc0e9b890d822", "created_at": "2026-11-01T15:40:05Z", "updated_at": "2026-11-01T18:47:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of cardiac myofilament protein isoforms using multiple mass spectrometry based approaches.", "doi": "10.1002/prca.201400039", "pmid": "24974818", "authors": ["Viola Kooij", "Vidya Venkatraman", "Jonathan A Kirk", "Ceereena Ubaida-Mohien", "David R Graham", "Matthijs J Faber", "Jennifer E Van Eyk"], "journal": "Proteomics. Clinical applications", "year": 2014, "abstract": "PURPOSE: The identification of protein isoforms in complex biological samples is challenging. We, therefore, used an MS approach to unambiguously identify cardiac myofilament protein isoforms based on the observation of a tryptic peptide consisting of a sequence unique to a particular isoform.\nEXPERIMENTAL DESIGN: Three different workflows were used to isolate and fractionate rat cardiac myofilament subproteomes. All fractions were analyzed on an LTQ-Orbitrap MS, proteins were identified using various search engines (MASCOT, X!Tandem, X!Tandem Kscore, and OMSSA) with results combined via PepArML Meta-Search engine, and a postsearch analysis was performed by MASPECTRAS. All MS data have been deposited in the ProteomeXchange with identifier PXD000874 (http://proteomecentral.proteomexchange.org/dataset/PXD000874).\nRESULTS: The combination of multiple workflows and search engines resulted in a larger number of nonredundant proteins identified than with individual methods. A total of 102 myofilament annotated proteins were observed overlapping in two or three of the workflows. Literature search for myofilament presence with manual validation of the MS spectra was carried out for unambiguous identification: ten cardiac myofilament and 17 cardiac myofilament-associated proteins were identified with 39 isoforms and subisoforms.\nCONCLUSION AND CLINICAL RELEVANCE: We have identified multiple isoforms of myofilament proteins that are present in cardiac tissue using unique tryptic peptides. Changes in distribution of these protein isoforms under pathological conditions could ultimately allow for clinical diagnostics or as therapeutic targets.", "claims": [{"id": "claim-target-result", "statement": "Using a 5% peptide false discovery rate for database searching and manual spectral validation, with source data deposited in the PRIDE partner repository of ProteomeXchange under dataset identifier PXD000874, the study identified a core set of 10 cardiac myofilament and 17 cardiac myofilament-associated proteins containing 39 isoforms and sub-isoforms.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:24974818", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 102 myofilament annotated proteins were observed overlapping in two or three of the workflows. Literature search for myofilament presence with manual validation of the MS spectra was carried out for unambiguous identification: 10 cardiac myofilament and 17 cardiac myofilament-associated proteins were identified with 39 isoforms and sub-isoforms."}, {"asset": "source:pmid:24974818", "locator": "sections[7] \"Database searching and processing\" paragraph 2", "quote": "The PepArML combined search results as well as the individual X!Tandem, Mascot and OMSSA search results were parsed and analyzed using MASPECTRAS 2 at a peptide false discovery rate (FDR) of 5% with proteins identified by one or more unique peptides [20]."}, {"asset": "source:pmid:24974818", "locator": "sections[7] \"Database searching and processing\" paragraph 2", "quote": "The MS spectrum-peptide match FDR was set to 1%, while the peptide-protein match FDR was set to 5%."}, {"asset": "source:pmid:24974818", "locator": "sections[7] \"Database searching and processing\" paragraph 2", "quote": "The mass spectrometry proteomics data has been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository [24] with the dataset identifier PXD000874."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using a 5% peptide false discovery rate for database searching and manual spectral validation, with source data deposited in the PRIDE partner repository of ProteomeXchange under dataset identifier PXD000874, the study identified a core set of 10 cardiac myofilament and 17 cardiac myofilament-associated proteins containing 39 isoforms and sub-isoforms.", "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:24974818"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:24974818", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/prca.201400039", "sha256": "sha256:d4f3be983e022d71867923df6a7e924fa0d74fcb34ffe70bb9aba552eda713cf", "bytes": 29654, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/prca.201400039", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4222538", "source": "ncbi_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), 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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": [], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:24974818"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:23Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": null}, "calls": 2, "usage": {"prompt_tokens": 14813, "completion_tokens": 1050, "cached_tokens": 528}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:24974818", "type": "paper", "label": "pmid:24974818"}, {"id": "source:pmid:24974818", "type": "manuscript", "label": "PMID 24974818 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:24974818", "type": "paper", "label": "pmid:24974818"}, {"id": "source:pmid:24974818", "type": "manuscript", "label": "PMID 24974818 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-24974818", "type": "extraction", "used": ["source:pmid:24974818"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:24974818", "parent_hash": "sha256:bce5db39cf39a2c2fb25e2ad883eba4f9a8700d1700f1766f6d41cc9acdd42b2", "fork_of": null, "generation": 4}, "gaps": ["execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["myofilament protein isoforms using multiple mass spectrometry based approaches."], "order_basis": "paper_text_order:26", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["rkflows were used to isolate and fractionate rat cardiac myofilament subproteomes. All fracti", "collected from 7-8 weeks old Sprague-Dawley Rats (Pel Freeze Biologicals). A single heart was", "ng Triton X-100 [10]. Briefly, tissue from a rat heart was homogenized in 75 mM KCl2, 2 mM Mg", "toplasmic and soluble proteins [9]. Briefly, rat heart tissue was homogenized at 4 °C at the"], "order_basis": "paper_text_order:440", "id": "assay:2"}]}