Empowering Shotgun Mass Spectrometry with 2DE: A HepG2 Study.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32471280", "kind": "science-record", "revision": 6, "content_hash": "sha256:f2bef350774ebb7be3d07bfd29a53d452f3c48f8a6fb58c9ee894acd049ec920", "created_at": "2026-11-01T15:41:02Z", "updated_at": "2026-11-01T21:23:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Empowering Shotgun Mass Spectrometry with 2DE: A HepG2 Study.", "doi": "10.3390/ijms21113813", "pmid": "32471280", "authors": ["Olga Kiseleva", "Elena Ponomarenko", "Ekaterina Poverennaya"], "journal": "International journal of molecular sciences", "year": 2020, "abstract": "One of the major goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to catalog and annotate a myriad of heterogeneous proteoforms, produced by ca. 20 thousand genes. To achieve a detailed and personalized understanding into proteomes, we suggest using a customized RNA-seq library of potential proteoforms, which includes aberrant variants specific to certain biological samples. Two-dimensional electrophoresis coupled with high-performance liquid chromatography allowed us to downgrade the difficulty of biological mixing following shotgun mass spectrometry. To benchmark the proposed pipeline, we examined heterogeneity of the HepG2 hepatoblastoma cell line proteome. Data are available via ProteomeXchange with identifier PXD018450.", "claims": [{"id": "claim-method", "statement": "To control the confidence of the identification, false discovery rates (FDR) were calculated in PeptideShaker by searching a decoy database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32471280", "locator": "sections[15] \"4.3. MS-Based Proteomics\" paragraph 4", "quote": "To control the confidence of the identification, false discovery rates (FDR) were calculated in PeptideShaker by searching a decoy database."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD018450.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32471280", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD018450."}], "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:32471280"], "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:PXD018450"], "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:PXD018450"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32471280", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms21113813", "sha256": "sha256:34a0cf2e7b5f75b99a92a41c4f30be7b77a97efc5496a267458c53a1631defff", "bytes": 44335, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms21113813", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7312985", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD018450", "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=PXD018450", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD018450", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD018450.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD018450.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomic profiling of HepG2 cell line after 2DE fractionation", "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:SRX390071", "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=SRX390071", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "SRX390071", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD018450.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD018450.", "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": "2026-10-31T18:35:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:SRX395473", "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=SRX395473", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "SRX395473", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD018450.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD018450.", "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": "2026-10-31T18:35:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD018450 not downloaded", "asset:data:geo:PXD018450 licence not read", "asset:data:geo:SRX390071 not downloaded", "asset:data:geo:SRX390071 licence not read", "asset:data:geo:SRX395473 not downloaded", "asset:data:geo:SRX395473 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "False discovery rate (FDR) control using a decoy database", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To control the confidence of the identification, false discovery rates (FDR) were calculated in PeptideShaker by searching a decoy database."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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 (False discovery rate (FDR) control using a decoy database), 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": ["SRX395473", "SRX390071", "PXD018450"], "resolved_accessions": ["PXD018450"], "statements": ["Data are available via ProteomeXchange with identifier PXD018450."], "basis": "The paper names PXD018450 in NCBI and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:32471280", "data:geo:PXD018450"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD018450"]}, "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": "2026-10-31T18:20:15Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 30298, "completion_tokens": 1776, "cached_tokens": 784}}, "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:32471280", "type": "paper", "label": "pmid:32471280"}, {"id": "source:pmid:32471280", "type": "manuscript", "label": "PMID 32471280 full text"}, {"id": "data:geo:PXD018450", "type": "dataset", "label": "GEO PXD018450"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32471280", "type": "paper", "label": "pmid:32471280"}, {"id": "source:pmid:32471280", "type": "manuscript", "label": "PMID 32471280 full text"}, {"id": "data:geo:PXD018450", "type": "dataset", "label": "GEO PXD018450"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32471280", "type": "extraction", "used": ["source:pmid:32471280"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD018450", "type": "accession_resolution", "used": ["data:geo:PXD018450"], "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:32471280", "parent_hash": "sha256:e32728695a2971917150ccfa2bba576c90440f9f516bfa0c4bbb906c6aa2697e", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD018450 licence not read", "asset:data:geo:PXD018450 not downloaded", "asset:data:geo:SRX390071 licence not read", "asset:data:geo:SRX390071 not downloaded", "asset:data:geo:SRX395473 licence not read", "asset:data:geo:SRX395473 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "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": 0.99, "evidence": ["Empowering Shotgun Mass Spectrometry with 2DE: A HepG2 Study.", "culty of biological mixing following shotgun mass spectrometry. To benchmark the proposed pipeline, we exam", "ary 1). Were compared the results of the 2DE-LC-MS/MS proteome profiling of the HepG2 cell line wi"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"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": ["wering Shotgun Mass Spectrometry with 2DE: A HepG2 Study.", "d pipeline, we examined heterogeneity of the HepG2 hepatoblastoma cell line proteome. Data are", "d 25 proteoforms. Using this strategy in the HepG2 cell line we identified 2358 proteoforms enc", "f the 2DE-LC-MS/MS proteome profiling of the HepG2 cell line with the panoramic MS profiling of"], "order_basis": "paper_text_order:4", "id": "assay:2"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["nto proteomes, we suggest using a customized RNA-seq library of potential proteoforms, which incl"], "order_basis": "paper_text_order:297", "id": "assay:3"}]}