Data on mass spectrometry-based proteomics for studying the involvement of CYLD in the ubiquitination events downstream of EGFR activation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29904688", "kind": "science-record", "revision": 6, "content_hash": "sha256:0c33b7036d1e9585a46f1d2241895f9cd113f38e9f85b6de8e64ed34c8091043", "created_at": "2026-11-01T15:40:34Z", "updated_at": "2026-11-01T21:21:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Data on mass spectrometry-based proteomics for studying the involvement of CYLD in the ubiquitination events downstream of EGFR activation.", "doi": "10.1016/j.dib.2018.04.049", "pmid": "29904688", "authors": ["Virginia Sanchez-Quiles", "Nerea Osinalde", "Vyacheslav Akimov", "Irina Kratchmarova", "Blagoy Blagoev"], "journal": "Data in brief", "year": 2018, "abstract": "The present data article corresponds to the proteomic data of the involvement of Cylindromatosis protein (CYLD) in the ubiquitination signaling initiated by EGF stimulation. CYLD tumor suppressor protein has Lys63-chain deubiquitinase activity that has been proved essential for the negative regulation of crucial signaling mechanisms, namely the NFkB pathway. Previous results have suggested the involvement of CYLD in the EGF-dependent signal transduction as well, showing its engagement within the tyrosine-phosphorylated complexes formed following the addition of the growth factor. EGFR signaling participates in central cellular processes and its tight regulation, partly through ubiquitination cascades, is decisive for a balanced cellular homeostasis. We carried out the substitution of the endogenous pool of ubiquitin for a His-FLAG-tagged ubiquitin (Stable Ubiquitin Exchange, StUbEx), in combination with the shRNA silencing of CYLD and SILAC-labeling on HeLa cells. The subsequent tandem affinity purification of ubiquitinated proteins in control and CYLD-depleted cells was followed by mass spectrometric analysis. Therefore, we present an unbiased study investigating the impact of CYLD in the EGF-dependent ubiquitination. The data supplied herein is related to the research article entitled \"Cylindromatosis tumor suppressor protein (CYLD) deubiquitinase is necessary for proper ubiquitination and degradation of the epidermal growth factor receptor\" (Sanchez-Quiles et al., 2017) [1]. We provide the associated mass spectrometry raw files, excel tables and gene ontology enrichments. The data have been deposited in the ProteomeXchange with the identifier PXD003423.", "claims": [{"id": "claim-method", "statement": "The calculation of significantly changed proteins was performed using the Perseus software [11].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29904688", "locator": "sections[10] \"Data analysis\" paragraph 2", "quote": "The calculation of significantly changed proteins was performed using the Perseus software [11]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the data presented in this article are deposited in the ProteomeXchange consortium via de identifier PXD003423 (http://www.proteomexchange.org/). The list of the identified and quantified proteins obtained in the two replicas of the study are provided in the supplementary material of this article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29904688", "locator": "sections[1] \"p\" paragraph 1", "quote": "All the data presented in this article are deposited in the ProteomeXchange consortium via de identifier PXD003423 (http://www.proteomexchange.org/). The list of the identified and quantified proteins obtained in the two replicas of the study are provided in the supplementary material of this article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper reports that “the deubiquitinase CYLD is necessary for the correct ubiquitination of the activated receptor in a counterintuitive manner.”", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29904688", "locator": "sections[2] \"p\" paragraph 1", "quote": "The workflow described herein resulted in the discovery of an unexpected role of CYLD in the signaling events downstream EGF stimulation, namely that the deubiquitinase CYLD is necessary for the correct ubiquitination of the activated receptor in a counterintuitive manner."}, {"asset": "source:pmid:29904688", "locator": "sections[10] \"Data analysis\" paragraph 2", "quote": "The calculation of significantly changed proteins was performed using the Perseus software [11]."}, {"asset": "source:pmid:29904688", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We provide the associated mass spectrometry raw files, excel tables and gene ontology enrichments. The data have been deposited in the ProteomeXchange with the identifier PXD003423."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper reports that “the deubiquitinase CYLD is necessary for the correct ubiquitination of the activated receptor in a counterintuitive manner.”", "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:29904688"], "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:PXD003423"], "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:PXD003423"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29904688", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2018.04.049", "sha256": "sha256:eee9e44f99567dd56fbe9b5cf453b27ce422052fa56f5565bb6e79cd9a73c25e", "bytes": 15484, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2018.04.049", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5997975", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD003423", "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=PXD003423", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD003423", "version": null, "note": "All the data presented in this article are deposited in the ProteomeXchange consortium via de identifier PXD003423 (http://www.proteomexchange.org/). The list of the identified and quantified proteins obtained in the two replicas of the study are provided in the supplementary material of this article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the data presented in this article are deposited in the ProteomeXchange consortium via de identifier PXD003423 (http://www.proteomexchange.org/). The list of the identified and quantified proteins obtained in the two replicas of the study are provided in the supplementary material of this article.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "EGF-dependent ubiquitinome, phosphorylation and interactome analysis in control and CYLD-deficient cells", "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:29904688:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:808ea76ec598e80dc3c9a00e89ab62915fb43fad47c0d13d377b4661dba689dd", "bytes": 1657, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0005", "version": null, "note": null, "structure": {"pmcid": "PMC5997975", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Cell signaling and ubiquitination"], ["More specific subject area", "EGFR Signaling and ubiquitinome"], ["Type of data", "Mass spectrometry (MS) data"], ["How data was acquired", "MS data was acquired on a Q-Exactive mass spectrometer (Thermo Scientific)."], ["Data format", "Raw and excel files"], ["Experimental factors", "Substitution of endogenous ubiquitin for a doubly-tagged version of ubiquitin in HeLa cells, combined with silencing of CYLD using shRNA and SILAC labeling of different conditions. shControl or shCYLD cells were either left starved or stimulated with EGF for 6 min."], ["Experimental features", "After the corresponding stimulation of shControl or shCYLD cells, protein extracts from two paralleled SILAC experiments were pooled accordingly and ubiquitinated proteins were enriched using a two steps procedure. An enrichment using Ni-NTA beads was performed, followed by immunoprecipitation of proteins using anti-FLAG specific antibodies. Enriched proteins were subjected to in-solution digestion and the resulting peptides were fractionated prior their LC–MS/MS analysis."], ["Data source location", "University of Southern Denmark, Odense, Denmark"], ["Data accessibility", "All the data presented in this article are deposited in the ProteomeXchange consortium via de identifier PXD003423 (http://www.proteomexchange.org/). The list of the identified and quantified proteins obtained in the two replicas of the study are provided in the supplementary material of this article."]], "row_count": 9, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:29904688:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:808ea76ec598e80dc3c9a00e89ab62915fb43fad47c0d13d377b4661dba689dd", "bytes": 1657, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0005", "version": null, "note": null, "structure": {"pmcid": "PMC5997975", "section_index": 2, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Cell signaling and ubiquitination"], ["More specific subject area", "EGFR Signaling and ubiquitinome"], ["Type of data", "Mass spectrometry (MS) data"], ["How data was acquired", "MS data was acquired on a Q-Exactive mass spectrometer (Thermo Scientific)."], ["Data format", "Raw and excel files"], ["Experimental factors", "Substitution of endogenous ubiquitin for a doubly-tagged version of ubiquitin in HeLa cells, combined with silencing of CYLD using shRNA and SILAC labeling of different conditions. shControl or shCYLD cells were either left starved or stimulated with EGF for 6 min."], ["Experimental features", "After the corresponding stimulation of shControl or shCYLD cells, protein extracts from two paralleled SILAC experiments were pooled accordingly and ubiquitinated proteins were enriched using a two steps procedure. An enrichment using Ni-NTA beads was performed, followed by immunoprecipitation of proteins using anti-FLAG specific antibodies. Enriched proteins were subjected to in-solution digestion and the resulting peptides were fractionated prior their LC–MS/MS analysis."], ["Data source location", "University of Southern Denmark, Odense, Denmark"], ["Data accessibility", "All the data presented in this article are deposited in the ProteomeXchange consortium via de identifier PXD003423 (http://www.proteomexchange.org/). The list of the identified and quantified proteins obtained in the two replicas of the study are provided in the supplementary material of this article."]], "row_count": 9, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:PXD003423 not downloaded", "asset:data:geo:PXD003423 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Perseus software, using significance B with p<0.001", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The calculation of significantly changed proteins was performed using the Perseus software [11]."}}], "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 (Perseus software, using significance B with p<0.001), 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": ["PXD003423"], "resolved_accessions": ["PXD003423"], "statements": ["All the data presented in this article are deposited in the ProteomeXchange consortium via de identifier PXD003423 (http://www.proteomexchange.org/). The list of the identified and quantified proteins obtained in the two replicas of the study are provided in the supplementary material of this article."], "basis": "The paper names PXD003423 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:29904688", "data:geo:PXD003423", "asset:table:pmid:29904688:1", "asset:table:pmid:29904688:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD003423"]}, "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": "2026-10-31T18:34:44Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 31975, "completion_tokens": 2892, "cached_tokens": 2114}}, "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:29904688", "type": "paper", "label": "pmid:29904688"}, {"id": "source:pmid:29904688", "type": "manuscript", "label": "PMID 29904688 full text"}, {"id": "data:geo:PXD003423", "type": "dataset", "label": "GEO PXD003423"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29904688", "type": "paper", "label": "pmid:29904688"}, {"id": "source:pmid:29904688", "type": "manuscript", "label": "PMID 29904688 full text"}, {"id": "data:geo:PXD003423", "type": "dataset", "label": "GEO PXD003423"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29904688", "type": "extraction", "used": ["source:pmid:29904688"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD003423", "type": "accession_resolution", "used": ["data:geo:PXD003423"], "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:29904688", "parent_hash": "sha256:91837c2e9db13d4b67e2957f8616d7ad34f3db77dec580f9ad56af0380f1abc3", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD003423 licence not read", "asset:data:geo:PXD003423 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": ["Data on mass spectrometry-based proteomics for studying the involvemen", "trol and CYLD-depleted cells was followed by mass spectrometric analysis. Therefore, we present an unbiased", "et al., 2017) [1]. We provide the associated mass spectrometry raw files, excel tables and gene ontology en", "the indicated times. Sample preparation for mass spectrometry analysis For the enrichment of ubiquitinated"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["n Exchange, StUbEx), in combination with the shRNA silencing of CYLD and SILAC-labeling on HeLa", "e performed. Firstly, HeLa-StUbEx cells were transfected with a shRNA construct for the stable downre", "y, HeLa-StUbEx cells were transfected with a shRNA construct for the stable downregulation of C"], "order_basis": "paper_text_order:1016", "id": "assay:2"}, {"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": ["hRNA silencing of CYLD and SILAC-labeling on HeLa cells. The subsequent tandem affinity purifi", "ineering strategies were performed. Firstly, HeLa-StUbEx cells were transfected with a shRNA c", "ication tools against the two tags. Finally, HeLa-StUbEx cells were metabolically labeled usin", "ssays Human cervix epithelial adenocarcinoma HeLa cells were grown in Dulbecco's modified Eagl"], "order_basis": "paper_text_order:1062", "id": "assay:3"}]}