The quantitative changes in the yeast Hsp70 and Hsp90 interactomes upon DNA damage.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26217697", "kind": "science-record", "revision": 8, "content_hash": "sha256:1d0ac33768c698a5062a8926bbfa6cde7a0910d4ee8ce2fb437913469630c65b", "created_at": "2026-11-01T15:40:09Z", "updated_at": "2026-11-01T22:42:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The quantitative changes in the yeast Hsp70 and Hsp90 interactomes upon DNA damage.", "doi": "10.1016/j.dib.2014.10.006", "pmid": "26217697", "authors": ["Andrew W Truman", "Kolbrun Kristjansdottir", "Donald Wolfgeher", "Natalia Ricco", "Anoop Mayampurath", "Samuel L Volchenboum", "Josep Clotet", "Stephen J Kron"], "journal": "Data in brief", "year": 2015, "abstract": "The molecular chaperones Hsp70 and Hsp90 participate in many important cellular processes, including how cells respond to DNA damage. Here we show the results of applied quantitative affinity-purification mass spectrometry (AP-MS) proteomics to understand the protein network through which Hsp70 and Hsp90 exert their effects on the DNA damage response (DDR). We characterized the interactomes of the yeast Hsp70 isoform Ssa1 and Hsp90 isoform Hsp82 before and after exposure to methyl methanesulfonate. We identified 256 chaperone interactors, 146 of which are novel. Although the majority of chaperone interaction remained constant under DNA damage, 5 proteins (Coq5, Ast1, Cys3, Ydr210c and Rnr4) increased in interaction with Ssa1 and/or Hsp82. This data presented here are related to [1] (Truman et al., in press). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaino et al. (2013) [2]) with the dataset identifier PXD001284.", "claims": [{"id": "claim-method", "statement": "An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26217697", "locator": "sections[9] \"LC–MS/MS data analysis, statistical analysis and visualization\" paragraph 3", "quote": "An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available with this article. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001284.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26217697", "locator": "sections[1] \"Specifications table\" paragraph 2", "quote": "Data are available with this article."}, {"asset": "source:pmid:26217697", "locator": "sections[1] \"Specifications table\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001284."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used ANOVA in R to assess significant variability between biological replicates, and the full source data were uploaded to the PRIDE repository under reference number PXD001284; the headline proteomics result was the identification of 256 chaperone interactors, including 146 novel interactors.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group."}, "evidence": [{"asset": "source:pmid:26217697", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We identified 256 chaperone interactors, 146 of which are novel."}, {"asset": "source:pmid:26217697", "locator": "sections[9] \"LC–MS/MS data analysis, statistical analysis and visualization\" paragraph 3", "quote": "Statistical analysis was performed using the R statistical package (http://www.r-project.org/)."}, {"asset": "source:pmid:26217697", "locator": "sections[9] \"LC–MS/MS data analysis, statistical analysis and visualization\" paragraph 3", "quote": "An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group."}, {"asset": "source:pmid:26217697", "locator": "sections[9] \"LC–MS/MS data analysis, statistical analysis and visualization\" paragraph 3", "quote": "The full data obtained was uploaded to the PRIDE repository and can now be found under reference number PXD001284."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used ANOVA in R to assess significant variability between biological replicates, and the full source data were uploaded to the PRIDE repository under reference number PXD001284; the headline proteomics result was the identification of 256 chaperone interactors, including 146 novel interactors.", "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:26217697"], "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:PXD001284"], "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:PXD001284"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26217697", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2014.10.006", "sha256": "sha256:b5683796349ebfa72523999f8523a751138ecc1c8ccf5721d356e06a0c779582", "bytes": 8982, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2014.10.006", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4459869", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD001284", "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=PXD001284", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD001284", "version": null, "note": "Data are available with this article. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001284.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available with this article. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001284.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "The Quantitative Changes in the Yeast Hsp70 and Hsp90 Interactomes upon DNA Damage", "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:26217697:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:407b1ebddeffac3dfb9c2b3d88277ccda58239ea12c167bb2a9623b67fb007ca", "bytes": 1016, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0005", "version": null, "note": null, "structure": {"pmcid": "PMC4459869", "section_index": 1, "section_title": "Specifications table", "row_count": 10, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Biology"], ["More specific subject area", "Molecular chaperones, Mass spectrometry, DNA damage response"], ["Type of data", "18O Quant LC–MS/MS Mass spectrometry data"], ["How data was acquired", "Mass spectrometry. Thermo LTQ Orbitrap XL"], ["Data format", "*.Raw"], ["Experimental factors", "Yeast cells expressing HIS6-tagged Ssa1 or Hsp82 were untreated or treated with 0.02% MMS for 3 h"], ["Experimental features", "HIS6-Ssa1 or HIS6-Hsp82 complexes were purified by IMAC and processed by mass spectrometry"], ["Data source location", "The University of Chicago, Chicago, IL, USA"], ["Data accessibility", "Data are available with this article."], ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001284."]], "row_count": 10, "column_count": 2, "numeric_cells": 4, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:PXD001284 not downloaded", "asset:data:geo:PXD001284 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": []}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["PXD001284"], "resolved_accessions": ["PXD001284"], "statements": ["Data are available with this article. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001284."], "basis": "The paper names PXD001284 in PRIDE partner repository, via the ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:26217697", "data:geo:PXD001284", "asset:table:pmid:26217697:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD001284"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:24:10Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "reordered"}, "calls": 8, "usage": {"prompt_tokens": 24600, "completion_tokens": 3097, "cached_tokens": 1552}}, "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:26217697", "type": "paper", "label": "pmid:26217697"}, {"id": "source:pmid:26217697", "type": "manuscript", "label": "PMID 26217697 full text"}, {"id": "data:geo:PXD001284", "type": "dataset", "label": "GEO PXD001284"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26217697", "type": "paper", "label": "pmid:26217697"}, {"id": "source:pmid:26217697", "type": "manuscript", "label": "PMID 26217697 full text"}, {"id": "data:geo:PXD001284", "type": "dataset", "label": "GEO PXD001284"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26217697", "type": "extraction", "used": ["source:pmid:26217697"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD001284", "type": "accession_resolution", "used": ["data:geo:PXD001284"], "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:26217697", "parent_hash": "sha256:5936b72bbec3ea0b2ca9087bae67bc4c1290ce5c6cb77c481dc740e5a5aee7c6", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD001284 licence not read", "asset:data:geo:PXD001284 not downloaded", "execution.not_run", "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": ["f applied quantitative affinity-purification mass spectrometry (AP-MS) proteomics to understand the protein", "elated to [1] (Truman et al., in press). The mass spectrometry proteomics data have been deposited to the P", "inity-purification mass spectrometry (AP-MS) proteomics to understand the protein network through wh", "man et al., in press). The mass spectrometry proteomics data have been deposited to the ProteomeXcha"], "order_basis": "paper_text_order:244", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["An ANOVA test was then performed to identify proteins that indicate significant variability (P-value<0.05) between biological replicates within each group."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}