Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25847399", "kind": "science-record", "revision": 6, "content_hash": "sha256:8b1eb2f477598b04fb4b6012ff580dace11385429ebc46fc9fdeac228683e59e", "created_at": "2026-11-01T15:40:07Z", "updated_at": "2026-11-01T21:19:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs.", "doi": "10.1007/s12192-015-0583-2", "pmid": "25847399", "authors": ["Andrija Finka", "Vishal Sood", "Manfredo Quadroni", "Paolo De Los Rios", "Pierre Goloubinoff"], "journal": "Cell stress & chaperones", "year": 2015, "abstract": "Classic semiquantitative proteomic methods have shown that all organisms respond to a mild heat shock by an apparent massive accumulation of a small set of proteins, named heat-shock proteins (HSPs) and a concomitant slowing down in the synthesis of the other proteins. Yet unexplained, the increased levels of HSP messenger RNAs (mRNAs) may exceed 100 times the ensuing relative levels of HSP proteins. We used here high-throughput quantitative proteomics and targeted mRNA quantification to estimate in human cell cultures the mass and copy numbers of the most abundant proteins that become significantly accumulated, depleted, or unchanged during and following 4 h at 41 °C, which we define as mild heat shock. This treatment caused a minor across-the-board mass loss in many housekeeping proteins, which was matched by a mass gain in a few HSPs, predominantly cytosolic HSPCs (HSP90s) and HSPA8 (HSC70). As the mRNAs of the heat-depleted proteins were not significantly degraded and less ribosomes were recruited by excess new HSP mRNAs, the mild depletion of the many housekeeping proteins during heat shock was attributed to their slower replenishment. This differential protein expression pattern was reproduced by isothermal treatments with Hsp90 inhibitors. Unexpectedly, heat-treated cells accumulated 55 times more new molecules of HSPA8 (HSC70) than of the acknowledged heat-inducible isoform HSPA1A (HSP70), implying that when expressed as net copy number differences, rather than as mere \"fold change\" ratios, new biologically relevant information can be extracted from quantitative proteomic data. Raw data are available via ProteomeXchange with identifier PXD001666.", "claims": [{"id": "claim-method", "statement": "The statistical analysis was performed with the R-statistical package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25847399", "locator": "sections[7] \"Biostatistical analysis\" paragraph 2", "quote": "The statistical analysis was performed with the R-statistical package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw data and the MaxQuant output are available via ProteomeXchange (http://proteomecentral.proteomexchange.org) with identifier PXD001666.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25847399", "locator": "sections[10] \"Data availability\" paragraph 2", "quote": "Raw data and the MaxQuant output are available via ProteomeXchange (http://proteomecentral.proteomexchange.org) with identifier PXD001666."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using SILAC quantitative proteomics and targeted mRNA quantification with R-based statistical analysis, mild heat shock caused a minor across-the-board mass loss in many housekeeping proteins that was matched by a mass gain in a few HSPs; the source data are available through ProteomeXchange under identifier PXD001666.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25847399", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This treatment caused a minor across-the-board mass loss in many housekeeping proteins, which was matched by a mass gain in a few HSPs, predominantly cytosolic HSPCs (HSP90s) and HSPA8 (HSC70)."}, {"asset": "source:pmid:25847399", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Raw data are available via ProteomeXchange with identifier PXD001666."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using SILAC quantitative proteomics and targeted mRNA quantification with R-based statistical analysis, mild heat shock caused a minor across-the-board mass loss in many housekeeping proteins that was matched by a mass gain in a few HSPs; the source data are available through ProteomeXchange under identifier PXD001666.", "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:25847399"], "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:PXD001666"], "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:PXD001666"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:25847399", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12192-015-0583-2", "sha256": "sha256:408957d6d4c749263269c19b5b9edeb69a541205571db393b7db2cf20af24e30", "bytes": 61708, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12192-015-0583-2", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4463922", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD001666", "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=PXD001666", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD001666", "version": null, "note": "Raw data and the MaxQuant output are available via ProteomeXchange (http://proteomecentral.proteomexchange.org) with identifier PXD001666.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Raw data and the MaxQuant output are available via ProteomeXchange (http://proteomecentral.proteomexchange.org) with identifier PXD001666.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD001666 not downloaded", "asset:data:geo:PXD001666 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "R-statistical package", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The statistical analysis was performed with the R-statistical package."}}], "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 (R-statistical package), 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": ["PXD001666"], "resolved_accessions": ["PXD001666"], "statements": ["Raw data and the MaxQuant output are available via ProteomeXchange (http://proteomecentral.proteomexchange.org) with identifier PXD001666."], "basis": "The paper names PXD001666 in ProteomeXchange and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:25847399", "data:geo:PXD001666"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD001666"]}, "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": "2026-10-31T18:23:42Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 119962, "completion_tokens": 3092, "cached_tokens": 1800}}, "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:25847399", "type": "paper", "label": "pmid:25847399"}, {"id": "source:pmid:25847399", "type": "manuscript", "label": "PMID 25847399 full text"}, {"id": "data:geo:PXD001666", "type": "dataset", "label": "GEO PXD001666"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:25847399", "type": "paper", "label": "pmid:25847399"}, {"id": "source:pmid:25847399", "type": "manuscript", "label": "PMID 25847399 full text"}, {"id": "data:geo:PXD001666", "type": "dataset", "label": "GEO PXD001666"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-25847399", "type": "extraction", "used": ["source:pmid:25847399"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD001666", "type": "accession_resolution", "used": ["data:geo:PXD001666"], "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:25847399", "parent_hash": "sha256:df156e57449540c2a0246d5162a11f7ce41643788c9d12f376ab71bbe1f28f19", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD001666 licence not read", "asset:data:geo:PXD001666 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": 0.77, "evidence": ["hat are caused by geldanamycin in Jurkat and HeLa cells. Mean of change in mass fraction of 50"], "order_basis": "paper_text_order:5608", "id": "assay:1"}]}