Exploring the HeLa Dark Mitochondrial Proteome.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32195257", "kind": "science-record", "revision": 5, "content_hash": "sha256:461cc3b2d88bf4d9c4421bbbd2351613523b30116589b1751a7642c5d5c56de2", "created_at": "2026-11-01T15:40:58Z", "updated_at": "2026-11-01T18:52:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the HeLa Dark Mitochondrial Proteome.", "doi": "10.3389/fcell.2020.00137", "pmid": "32195257", "authors": ["Federica Marini", "Victor Corasolla Carregari", "Viviana Greco", "Maurizio Ronci", "Federica Iavarone", "Silvia Persichilli", "Massimo Castagnola", "Andrea Urbani", "Luisa Pieroni"], "journal": "Frontiers in cell and developmental biology", "year": 2020, "abstract": "In the framework of the Human Proteome Project initiative, we aim to improve mapping and characterization of mitochondrial proteome. In this work we implemented an experimental workflow, combining classical biochemical enrichments and mass spectrometry, to pursue a much deeper definition of mitochondrial proteome and possibly mine mitochondrial uncharacterized dark proteins. We fractionated in two compartments mitochondria enriched from HeLa cells in order to annotate 4230 proteins in both fraction by means of a multiple-enzyme digestion (trypsin, chymotrypsin and Glu-C) followed by mass spectrometry analysis using a combination of Data Dependent Acquisition (DDA) and Data Independent Acquisition (DIA). We detected 22 mitochondrial dark proteins not annotated for their function and we provide their relative abundance inside the mitochondrial organelle. Considering this work as a pilot study we expect that the same approach, in different biological system, could represent an advancement in the characterization of the human mitochondrial proteome providing uncharted ground to explore the mitonuclear phenotypic relationships. All spectra have been deposited to ProteomeXchange with PXD014201 and PXD014200 identifier.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry datasets generated for this study can be found in the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD014200 and PXD014201.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32195257", "locator": "sections[7] \"Data Availability Statement\" paragraph 2", "quote": "The mass spectrometry datasets generated for this study can be found in the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD014200 and PXD014201."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32195257"], "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:PXD014200"], "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:PXD014200"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32195257", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcell.2020.00137", "sha256": "sha256:61c043075067ce26b5585ed62ecbeecc90942793b497430c9c5d7d1d04c9ceeb", "bytes": 30355, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcell.2020.00137", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7066081", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD014200", "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=PXD014200", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD014200", "version": null, "note": "The mass spectrometry datasets generated for this study can be found in the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD014200 and PXD014201.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry datasets generated for this study can be found in the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD014200 and PXD014201.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Exploring the HeLa Dark Mitochondrial proteome", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD014201", "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=PXD014201", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD014201", "version": null, "note": "The mass spectrometry datasets generated for this study can be found in the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD014200 and PXD014201.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry datasets generated for this study can be found in the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD014200 and PXD014201.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Exploring the HeLa Dark Mitochondrial proteome", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD007053", "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=PXD007053", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD007053", "version": null, "note": "The mass spectrometry datasets generated for this study can be found in the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD014200 and PXD014201.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry datasets generated for this study can be found in the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD014200 and PXD014201.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32195257:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e00d6dfa07749b4d7fcc382a9d3464e4e32bbe4631be8f3ad24e8ca109ed831a", "bytes": 2912, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#T1", "version": null, "note": "List of mt-dark proteins identified in HeLa dataset.", "structure": {"pmcid": "PMC7066081", "section_index": 5, "section_title": "Mapping and Quantifying the Mitochondrial uPE1 Proteins", "row_count": 23, "column_count": 8}, "table": {"label": "TABLE 1", "caption": "List of mt-dark proteins identified in HeLa dataset.", "rows": [["Accession", "Description", "Mito evidence IMPI", "Mito localization IMPI", "HPA cell localization", "Enzyme", "Exp. fraction", "Gravy score"], ["NX_O60941-1", "Dystrobrevin beta", "Predicted", "Unknown", "Mitochondria (A)", "Try; Glu-C", "F1, F2", "−0.55"], ["NX_Q3SXM5-1", "Inactive hydroxysteroid dehydrogenase-like protein 1", "Known", "OM", "Intracellular, Membrane (P)", "Chym; Try", "F2", "+0.15"], ["NX_Q4VC31-1", "Coiled-coil domain-containing protein 58", "Known", "IMS", "Nucleoli, Mitochondria (A)", "Try; Chym; Glu-C", "F2", "−0.60"], ["NX_Q56VL3-1", "OCIA domain-containing protein 2", "Known", "Unknown", "Mitochondria (E)", "Try", "F2", "−0.26"], ["NX_Q8IYQ7-1", "Threonine synthase-like 1", "Known", "Matrix", "Nuclear bodies (A), Mitochondria (A), Cytosol (A)", "Try", "F2", "−0.13"], ["NX_Q8NFV4-1", "Protein ABHD11", "Known", "Matrix", "Mitochondria (S)", "Try; Chym", "F2", "−0.09"], ["NX_Q96EX1-1", "Small integral membrane protein 12", "Predicted", "Unknown", "Mitochondria (A)", "Try", "F2", "−0.53"], ["NX_Q96C01-1", "Protein FAM136A", "Known", "IMS", "Mitochondria (A)", "Try; Glu-C", "F2", "−0.43"], ["NX_Q96ER9-1", "Coiled-coil domain-containing protein 51", "Known", "Matrix", "Nucleosome (S), Mitochondria (S) Centrosome (A)", "Try; Glu-C", "F2", "−0.38"], ["NX_P56378-1", "6.8 kDa mitochondrial proteolipid", "Known", "IM", "Mitochondria (S),Nucleoli (S)", "Try", "F1,F2", "−0.02"], ["NX_Q9GZT6-1", "Coiled-coil domain-containing protein 90B", "Known", "Matrix", "Mitochondria (E)", "Try; Glu-C", "F2", "−0.55"], ["NX_A8MTT3-1", "Protein CEBPZOS", "Known", "IMS", "Nucleoplasm (A)", "Try; Glu-C", "F2", "−0.27"], ["NX_Q9H4I3-1", "TraB domain-containing protein", "Known", "OM", "Nucleus (A), Mitochondria (A)", "Try", "F2", "−0.21"], ["NX_Q9UFN0-1", "Protein NipSnap homolog 3A", "Known", "Matrix", "not available", "Try; Glu-C", "F2", "−0.37"], ["NX_Q6P1 × 6-1", "UPF0598 protein C8orf82", "Known", "Matrix", "Nucleus (A)", "Try; Chym", "F2", "−0.23"], ["NX_Q8N2U0-1", "Transmembrane protein 256", "Predicted", "Unknown", "Vesicles (A)", "Try", "F2", "+0.46"], ["NX_Q8WVI0-1", "Small integral membrane protein 4", "Predicted", "Unknown", "Nucleoplasm (A), Mitochondria (A)", "Try", "F2", "−0.54"], ["NX_Q8WW59-1", "SPRY domain-containing protein 4", "Known", "Matrix", "Nucleoplasm (A)", "Try", "F1,F2", "−0.07"], ["NX_Q96BQ5-1", "Coiled-coil domain-containing protein 127", "Known", "OM/IMS", "Nucleus (S), Nucleoli (S)", "Try; Chym", "F1,F2", "−0.72"], ["NX_Q96DB5-1", "Regulator of microtubule dynamics protein 1", "Known", "OM/IMS", "Centrosomes (S),Actin filaments (S)", "Try", "F1,F2", "−0.37"], ["NX_Q96KF7-1", "Small integral membrane protein 8", "Known", "OM", "Vesicles (A)", "Try; Chym", "F2", "−0.55"], ["NX_Q9NU23-1", "LYR motif-containing protein 2", "Known", "matrix", "Cytosol (A)", "Try", "F2", "−0.70"]], "row_count": 23, "column_count": 8, "numeric_cells": 63, "header_rows": 1, "locator": "section[5]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32195257:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b9a2cf487f7f3aeb302d4b3d539a1b880e5b6274a39b8be378cc477122be73c6", "bytes": 2742, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[2]#T2", "version": null, "note": "Distribution of uPE1 mt-dark proteins identified in PXD007053 repository database.", "structure": {"pmcid": "PMC7066081", "section_index": 5, "section_title": "Mapping and Quantifying the Mitochondrial uPE1 Proteins", "row_count": 23, "column_count": 12}, "table": {"label": "TABLE 2", "caption": "Distribution of uPE1 mt-dark proteins identified in PXD007053 repository database.", "rows": [["Accession", "Description", "BJ", "HeLa", "H28", "Hek293", "HepG2", "HUVEC", "MDA-MB 231", "Thp1", "U2OS", "SH-SY5Y"], ["NX_O60941-1", "Dystrobrevin beta", "–", "–", "–", "–", "–", "–", "–", "–", "–", "–"], ["NX_Q3SXM5-1", "Inactive hydroxysteroid dehydrogenase-like protein 1", "–", "–", "–", "√", "√", "–", "–", "–", "–", "–"], ["NX_Q4VC31-1", "Coiled-coil domain-containing protein 58", "–", "–", "", "√", "√", "–", "√", "", "–", "–"], ["NX_Q56VL3-1", "OCIA domain-containing protein 2", "–", "√", "√", "–", "–", "√", "√", "√", "√", ""], ["NX_Q8IYQ7-1", "Threonine synthase-like 1", "–", "–", "–", "√", "–", "–", "√", "√", "–", "–"], ["NX_Q8NFV4-1", "Protein ABHD11", "–", "–", "–", "–", "√", "–", "√", "√", "–", "–"], ["NX_Q96EX1-1", "Small integral membrane protein 12", "–", "–", "–", "–", "–", "–", "–", "–", "–", "–"], ["NX_Q96C01-1", "Protein FAM136A", "–", "–", "–", "√", "√", "–", "–", "√", "–", "–"], ["NX_Q96ER9-1", "Coiled-coil domain-containing protein 51", "–", "–", "–", "√", "", "–", "–", "–", "–", "–"], ["NX_P56378-1", "6.8 kDa mitochondrial proteolipid", "–", "–", "–", "–", "–", "–", "–", "–", "–", "–"], ["NX_Q9GZT6-1", "Coiled-coil domain-containing protein 90B", "–", "–", "√", "–", "–", "–", "–", "–", "–", "–"], ["NX_A8MTT3-1", "Protein CEBPZOS", "–", "–", "–", "–", "–", "–", "–", "–", "–", "–"], ["NX_Q9H4I3-1", "TraB domain-containing protein", "–", "–", "√", "–", "–", "√", "–", "√", "–", "–"], ["NX_Q9UFN0-1", "Protein NipSnap homolog 3A", "–", "–", "√", "–", "–", "–", "√", "√", "√", "–"], ["NX_Q6P1 × 6-1", "UPF0598 protein C8orf82", "–", "–", "–", "√", "√", "–", "√", "√", "√", "–"], ["NX_Q8N2U0-1", "Transmembrane protein 256", "–", "–", "–", "–", "–", "–", "–", "–", "–", "–"], ["NX_Q8WVI0-1", "Small integral membrane protein 4", "–", "–", "–", "–", "–", "–", "–", "–", "–", "–"], ["NX_Q8WW59-1", "SPRY domain-containing protein 4", "–", "–", "–", "√", "√", "–", "–", "–", "–", "–"], ["NX_Q96BQ5-1", "Coiled-coil domain-containing protein 127", "–", "–", "√", "–", "–", "–", "–", "–", "–", "–"], ["NX_Q96DB5-1", "Regulator of microtubule dynamics protein 1", "–", "–", "√", "√", "–", "–", "√", "√", "–", "–"], ["NX_Q96KF7-1", "Small integral membrane protein 8", "–", "–", "–", "–", "–", "–", "–", "–", "–", "–"], ["NX_Q9NU23-1", "LYR motif-containing protein 2", "–", "–", "–", "–", "–", "–", "–", "–", "–", "–"]], "row_count": 23, "column_count": 12, "numeric_cells": 44, "header_rows": 1, "locator": "section[5]/table-wrap[2]#T2"}}], "gaps": ["asset:data:geo:PXD014200 not downloaded", "asset:data:geo:PXD014200 licence not read", "asset:data:geo:PXD014201 not downloaded", "asset:data:geo:PXD014201 licence not read", "asset:data:geo:PXD007053 not downloaded", "asset:data:geo:PXD007053 licence not read"]}, "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": "method", "blocked_on": "method:not_determinable", "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": "R1", "reachable": true, "accessions": ["PXD014200", "PXD014201", "PXD007053"], "resolved_accessions": ["PXD014200", "PXD014201"], "statements": ["The mass spectrometry datasets generated for this study can be found in the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD014200 and PXD014201."], "basis": "The paper names PXD014200, PXD014201 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:32195257", "data:geo:PXD014200", "asset:table:pmid:32195257:1", "asset:table:pmid:32195257:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD014200"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:18:48Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 22429, "completion_tokens": 1214, "cached_tokens": 512}}, "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:32195257", "type": "paper", "label": "pmid:32195257"}, {"id": "source:pmid:32195257", "type": "manuscript", "label": "PMID 32195257 full text"}, {"id": "data:geo:PXD014200", "type": "dataset", "label": "GEO PXD014200"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32195257", "type": "paper", "label": "pmid:32195257"}, {"id": "source:pmid:32195257", "type": "manuscript", "label": "PMID 32195257 full text"}, {"id": "data:geo:PXD014200", "type": "dataset", "label": "GEO PXD014200"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32195257", "type": "extraction", "used": ["source:pmid:32195257"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD014200", "type": "accession_resolution", "used": ["data:geo:PXD014200"], "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:32195257", "parent_hash": "sha256:1a7336c2d666d2ab2a6b18b914e9089367f314bb30b92964dc341963b09399c9", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:PXD007053 licence not read", "asset:data:geo:PXD007053 not downloaded", "asset:data:geo:PXD014200 licence not read", "asset:data:geo:PXD014200 not downloaded", "asset:data:geo:PXD014201 licence not read", "asset:data:geo:PXD014201 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Exploring the HeLa Dark Mitochondrial Proteome.", "two compartments mitochondria enriched from HeLa cells in order to annotate 4230 proteins in", "iefly, after isolating the mitochondria from HeLa cells (Alberio et al., 2017), we performed a"], "order_basis": "paper_text_order:0", "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": ["bining classical biochemical enrichments and mass spectrometry, to pursue a much deeper definition of mitoc", "trypsin, chymotrypsin and Glu-C) followed by mass spectrometry analysis using a combination of Data Depende", "lap of the lists of proteins IDs detected by LC-MS/MS experiments upon proteolytic digestion with"], "order_basis": "paper_text_order:238", "id": "assay:2"}]}